├── .gitignore ├── LICENSE.txt ├── README.md ├── docs ├── .nojekyll ├── 00_README.txt ├── Makefile ├── build │ └── html │ │ ├── .buildinfo │ │ ├── _images │ │ └── spec_uses.jpg │ │ ├── _sources │ │ ├── api_usage.rst.txt │ │ ├── index.rst.txt │ │ └── specification_language.rst.txt │ │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── jquery-3.1.0.js │ │ ├── jquery.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── spec_uses.jpg │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── api_usage.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── search.html │ │ ├── searchindex.js │ │ └── specification_language.html ├── index.html ├── make.bat └── source │ ├── _static │ └── spec_uses.jpg │ ├── api_usage.rst │ ├── conf.py │ ├── index.rst │ └── specification_language.rst ├── examples ├── 0_README.txt ├── create_scripts │ ├── 0_README.txt │ ├── abstract_feature.py │ ├── analysis_e.py │ ├── annotations.py │ ├── behavior-e.py │ ├── behavior.py │ ├── closed_interface-e.py │ ├── crcns_alm-1.py │ ├── crcns_hc-3.py │ ├── crcns_ret-1.py │ ├── crcns_ssc-1.py │ ├── custom_link.py │ ├── extensions │ │ ├── 0_README.txt │ │ ├── e-analysis.py │ │ ├── e-behavior.py │ │ ├── e-closed_interface.py │ │ ├── e-genJson.py │ │ ├── e-general.py │ │ ├── e-interface.py │ │ ├── e-interval.py │ │ ├── e-intracellular.py │ │ ├── e-link_test.py │ │ ├── e-module.py │ │ ├── e-timeseries.py │ │ ├── e-trajectorySeries.py │ │ └── e-trajectorySeries2.py │ ├── extracellular_ephys.py │ ├── extracellular_spikes.py │ ├── general-e.py │ ├── interface-e.py │ ├── interval-e.py │ ├── interval.py │ ├── intracellular-e.py │ ├── link_test-e.py │ ├── module-e.py │ ├── motion_correction.py │ ├── motion_correction2.py │ ├── run_all.sh │ ├── timeseries-e.py │ ├── trajectorySeries-e.py │ └── trajectorySeries2-e.py ├── created_nwb_files │ └── 0_README.txt ├── text_output_files │ ├── 0_README.txt │ ├── create │ │ └── 0_README.txt │ ├── diff │ │ └── 0_README.txt │ ├── doc │ │ └── 0_README.txt │ └── validate │ │ └── 0_README.txt └── utility_scripts │ ├── 0_README.txt │ ├── check_schemas.sh │ ├── cmp_created.sh │ ├── h5diffsig.sh │ ├── install_source_data.py │ ├── make_cv_diff.sh │ ├── make_docs.py │ ├── make_docs.sh │ ├── make_h5sig.py │ ├── make_pdf_doc.sh │ ├── validate_all.py │ ├── validate_behavior.py │ ├── validate_internal.sh │ └── validate_others.sh ├── matlab_bridge ├── 0_INSTALL.txt ├── 0_README.txt ├── matlab_bridge_api │ ├── +h5g8 │ │ ├── dataset.m │ │ ├── file.m │ │ ├── group.m │ │ └── node.m │ ├── nwb_file.m │ ├── nwb_utils.m │ ├── parse_arguments.m │ └── test_nwb.m ├── matlab_examples │ ├── 0_README.txt │ ├── create_scripts │ │ ├── 0_README.txt │ │ ├── abstract_feature.m │ │ ├── analysis_e.m │ │ ├── crcns_alm_1.m │ │ └── run_all_examples.m │ └── created_nwb_files │ │ └── 0_README.txt └── matlab_unittest │ ├── run_all_tests.m │ ├── t_annotation.m │ ├── t_append.m │ ├── t_array_layout.m │ ├── t_epoch_tag.m │ ├── t_general_ephys.m │ ├── t_general_image.m │ ├── t_general_opto.m │ ├── t_general_patch.m │ ├── t_general_species.m │ ├── t_general_top.m │ ├── t_if_add_ts.m │ ├── t_if_isi.m │ ├── t_modification_time.m │ ├── t_no_data.m │ ├── t_no_time.m │ ├── t_ref_image.m │ ├── t_softlink.m │ ├── t_starting_time.m │ ├── t_timeseries_link.m │ ├── t_top_datasets.m │ ├── t_unittimes.m │ ├── test_utils.m │ └── test_utils.py ├── nwb ├── __init__.py ├── check_schema.py ├── combine_messages.py ├── display_versions.py ├── doc_tools.py ├── find_links.py ├── h5diffsig.py ├── h5gate.py ├── make_docs.py ├── make_json.py ├── meta_schema.py ├── nwb_core.py ├── nwb_file.py ├── nwb_init.py ├── nwb_utils.py ├── suggest_spellings.py ├── validate.py └── value_summary.py ├── setup.py ├── test_all ├── 0_README.txt ├── make_curr.sh ├── make_dirsig.py ├── orig │ └── dirsig.txt ├── set_orig.py ├── show_diff.py ├── test_all.cfg └── test_all.sh └── unittest ├── 0_README.txt ├── run_tests.sh ├── t_annotation.py ├── t_append.py ├── t_array_layout.py ├── t_epoch_tag.py ├── t_general_ephys.py ├── t_general_image.py ├── t_general_opto.py ├── t_general_patch.py ├── t_general_species.py ├── t_general_top.py ├── t_if_add_ts.py ├── t_if_isi.py ├── t_modification_time.py ├── t_no_data.py ├── t_no_time.py ├── t_ref_image.py ├── t_region_reference.py ├── t_softlink.py ├── t_starting_time.py ├── t_strings.py ├── t_timeseries_link.py ├── t_top_datasets.py ├── t_unittimes.py └── test_utils.py /.gitignore: -------------------------------------------------------------------------------- 1 | # Optional source data downloaded separately 2 | /examples/source_data/crcns_* 3 | /examples/source_data_2/ 4 | 5 | # Generated output from tests 6 | examples/text_output_files/create/*txt 7 | examples/text_output_files/validate/*txt 8 | matlab_bridge/matlab_examples/text_output_files/ 9 | matlab_bridge/matlab_examples/created_nwb_files/ 10 | test_all/curr/ 11 | test_all/orig/ 12 | test_all/orig_bk*/ 13 | 14 | # Created nwb files 15 | *.nwb 16 | 17 | 18 | # Byte-compiled / optimized / DLL files 19 | __pycache__/ 20 | *.py[cod] 21 | *$py.class 22 | 23 | # C extensions 24 | *.so 25 | 26 | # Distribution / packaging 27 | .Python 28 | env/ 29 | build/ 30 | develop-eggs/ 31 | dist/ 32 | downloads/ 33 | eggs/ 34 | .eggs/ 35 | lib/ 36 | lib64/ 37 | parts/ 38 | sdist/ 39 | var/ 40 | *.egg-info/ 41 | .installed.cfg 42 | *.egg 43 | 44 | # PyInstaller 45 | # Usually these files are written by a python script from a template 46 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 47 | *.manifest 48 | *.spec 49 | 50 | # Installer logs 51 | pip-log.txt 52 | pip-delete-this-directory.txt 53 | 54 | # Unit test / coverage reports 55 | htmlcov/ 56 | .tox/ 57 | .coverage 58 | .coverage.* 59 | .cache 60 | nosetests.xml 61 | coverage.xml 62 | *,cover 63 | 64 | # Translations 65 | *.mo 66 | *.pot 67 | 68 | # Django stuff: 69 | *.log 70 | 71 | # Sphinx documentation 72 | docs/_build/ 73 | 74 | # PyBuilder 75 | target/ 76 | 77 | 78 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | Copyright (c) 2015 Allen Institute, California Institute of Technology, New York University School 2 | of Medicine, the Howard Hughes Medical Institute, University of California, Berkeley, GE, the Kavli 3 | Foundation and the International Neuroinformatics Coordinating Facility. All rights reserved. 4 | 5 | Redistribution and use in source and binary forms, with or without modification, are permitted 6 | provided that the following conditions are met: 7 | 8 | 1. Redistributions of source code must retain the above copyright notice, 9 | this list of conditions and the following disclaimer. 10 | 11 | 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and 12 | the following disclaimer in the documentation and/or other materials provided with the distribution. 13 | 14 | 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or 15 | promote products derived from this software without specific prior written permission. 16 | 17 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED 18 | WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 19 | PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR 20 | ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT 21 | LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 22 | INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR 23 | TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF 24 | ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 25 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Python (and Matlab) API for Neurodata Without Borders (NWB) format 2 | 3 | HTML formatted documentation about this API (including installation instructions) are at: 4 | http://neurodatawithoutborders.github.io/api-python 5 | 6 | Documentation in other formats (such as PDF) may be generated using the files in the ``docs`` 7 | directory. This is described in file ``docs/0_README.txt``. 8 | 9 | -------------------------------------------------------------------------------- /docs/.nojekyll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NeurodataWithoutBorders/api-python/52e97e7642021913ae6505ab63b7cc77d2622d76/docs/.nojekyll -------------------------------------------------------------------------------- /docs/00_README.txt: -------------------------------------------------------------------------------- 1 | This directory contains documentation for the NWB Python (and Matlab) API. 2 | The documentation can be built on Unix-like systems by entering: 3 | 4 | "make html" - to make html documentation 5 | "make latexpdf" - to make PDF documentation 6 | "make" - to see the different types of documentation available 7 | 8 | On Windows systems, "make.bat" can be used to generate documentation. 9 | 10 | Documentation will be created in directory "build". 11 | 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SPHINXPROJ = NWBAPI-Python 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -------------------------------------------------------------------------------- /docs/build/html/.buildinfo: -------------------------------------------------------------------------------- 1 | # Sphinx build info version 1 2 | # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. 3 | config: f97f3f0445b07afce5a7af1c7a109867 4 | tags: 645f666f9bcd5a90fca523b33c5a78b7 5 | -------------------------------------------------------------------------------- /docs/build/html/_images/spec_uses.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NeurodataWithoutBorders/api-python/52e97e7642021913ae6505ab63b7cc77d2622d76/docs/build/html/_images/spec_uses.jpg -------------------------------------------------------------------------------- /docs/build/html/_sources/index.rst.txt: -------------------------------------------------------------------------------- 1 | .. NWB API-Python documentation master file, created by 2 | sphinx-quickstart on Mon May 1 15:37:19 2017. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | NWB API-Python documentation 7 | ============================ 8 | 9 | | This documentation describes the NWB Python (and Matlab) API available at: 10 | | https://github.com/NeurodataWithoutBorders/api-python 11 | 12 | Contents 13 | -------- 14 | 15 | .. toctree:: 16 | :maxdepth: 2 17 | :numbered: 18 | 19 | api_usage 20 | specification_language 21 | 22 | 23 | 24 | .. 25 | Below are commeneted out for now 26 | Indices and tables 27 | ================== 28 | 29 | * :ref:`genindex` 30 | * :ref:`modindex` 31 | * :ref:`search` 32 | -------------------------------------------------------------------------------- /docs/build/html/_static/ajax-loader.gif: -------------------------------------------------------------------------------- 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99 | 100 | 101 | 102 | 103 | 104 | -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=source 11 | set BUILDDIR=build 12 | set SPHINXPROJ=NWBAPI-Python 13 | 14 | if "%1" == "" goto help 15 | 16 | %SPHINXBUILD% >NUL 2>NUL 17 | if errorlevel 9009 ( 18 | echo. 19 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 20 | echo.installed, then set the SPHINXBUILD environment variable to point 21 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 22 | echo.may add the Sphinx directory to PATH. 23 | echo. 24 | echo.If you don't have Sphinx installed, grab it from 25 | echo.http://sphinx-doc.org/ 26 | exit /b 1 27 | ) 28 | 29 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% 30 | goto end 31 | 32 | :help 33 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% 34 | 35 | :end 36 | popd 37 | -------------------------------------------------------------------------------- /docs/source/_static/spec_uses.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NeurodataWithoutBorders/api-python/52e97e7642021913ae6505ab63b7cc77d2622d76/docs/source/_static/spec_uses.jpg -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- 1 | .. NWB API-Python documentation master file, created by 2 | sphinx-quickstart on Mon May 1 15:37:19 2017. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | NWB API-Python documentation 7 | ============================ 8 | 9 | | This documentation describes the NWB Python (and Matlab) API available at: 10 | | https://github.com/NeurodataWithoutBorders/api-python 11 | 12 | Contents 13 | -------- 14 | 15 | .. toctree:: 16 | :maxdepth: 2 17 | :numbered: 18 | 19 | api_usage 20 | specification_language 21 | 22 | 23 | 24 | .. 25 | Below are commeneted out for now 26 | Indices and tables 27 | ================== 28 | 29 | * :ref:`genindex` 30 | * :ref:`modindex` 31 | * :ref:`search` 32 | -------------------------------------------------------------------------------- /examples/0_README.txt: -------------------------------------------------------------------------------- 1 | 0_README.txt for NWB examples 2 | 3 | 4 | Directories are: 5 | 6 | create_scripts - scripts used to create sample NWB files 7 | 8 | created_nwb_files - location of where example NWB files will be created 9 | 10 | utility_scripts - scripts demonstrating validating files and 11 | generating documentation. 12 | 13 | text_output_files - text files created when running create scripts or 14 | utility scripts. 15 | 16 | source_data_2 - This is initially absent. When added, it contains 17 | source data that is needed to run scripts that have prefix "crcns_". 18 | The "sourc_data_2" directory can be installed by 19 | running "get_source_data.py" in the utility_scripts directory. 20 | To install manually, download file "source_data_2.tar.gz" from: 21 | https://portal.nersc.gov/project/crcns/download/nwb-1 22 | then upack it, and put it in this directory. 23 | After adding it, the "source_data_2" directory should have subdirectories: 24 | crcns_alm-1 crcns_hc-3 crcns_ret-1 crcns_ssc-1 25 | 26 | To run the create_scripts, or the utility_scripts, cd into the corresponding 27 | directory and follow the instructions in the readme file in that directory. 28 | 29 | -------------------------------------------------------------------------------- /examples/create_scripts/0_README.txt: -------------------------------------------------------------------------------- 1 | This directory "examples/scripts" contains example 2 | scripts to create example NWB files. 3 | 4 | To run scripts individually, type: 5 | python 6 | 7 | To run all of the scripts, type: 8 | ./run_all_examples.sh 9 | 10 | Several types of scripts require additional files. These are: 11 | 12 | 13 | (1) Scripts that required input data. 14 | 15 | Scripts with with name starting with "crcns") require data in the 16 | "../examples/source_data" directory. This data must be downloaded 17 | and placed inside the ../source_data directory. Instructions 18 | for doing this are in the examples/0_README.txt file 19 | (i.e. the readme in the directory above this one). 20 | 21 | 22 | (2) Scripts that require extensions. 23 | 24 | Scripts that have name ending with "-e.py" require one or more "extensions" 25 | (files that define extensions to the NWB format). The extensions are 26 | stored in directory "extensions". Usually the name of the extension 27 | used with the script will be the same as the name of the create script, 28 | except "e-" will be in front of the extension. 29 | 30 | The convention of having "e-" in front of the extension (and "-e" at the 31 | end of the create script name) is only used for these examples. Any name for the 32 | create script and extension(s) can be used as long as the actual name of the 33 | extension(s) are referenced by the create script and passed as parameters to 34 | nwb_validate.py when validating NWB files created using one or more extensions. -------------------------------------------------------------------------------- /examples/create_scripts/analysis_e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as ut 5 | 6 | 7 | """ 8 | This example illustrates using an extension to store data in the the /analysis group. 9 | The /analysis group is reserved for results of lab-specific analysis. 10 | 11 | The extension definition is in file "extensions/e-analysis.py". 12 | 13 | The example is based on the contents of the Allen Institute for Brain Science 14 | Cell Types database NWB files. 15 | 16 | """ 17 | 18 | OUTPUT_DIR = "../created_nwb_files/" 19 | file_name = __file__[0:-3] + ".nwb" 20 | ######################################################################## 21 | # create a new NWB file 22 | settings = {} 23 | settings["file_name"] = OUTPUT_DIR + file_name 24 | settings["identifier"] = ut.create_identifier("example /analysis group using extension.") 25 | settings["mode"] = "w" 26 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 27 | settings["description"] = ("Test file demonstrating storing data in the /analysis group " 28 | "that is defined by an extension.") 29 | 30 | # specify the extension (Could be more than one. Only one used now). 31 | settings['extensions'] = ["extensions/e-analysis.py"] 32 | 33 | # create the NWB file object. this manages the file 34 | print("Creating " + settings["file_name"]) 35 | f = nwb_file.open(**settings) 36 | 37 | ######################################################################## 38 | # This example, stores spike times for multiple sweeps 39 | # create the group for the spike times 40 | # The group ("aibs_spike_times") is defined in the extension 41 | 42 | ast = f.make_group("aibs_spike_times") 43 | 44 | # some sample data 45 | times = [1.1, 1.2, 1.3, 1.4, 1.5] 46 | 47 | # create some sample sweeps 48 | for i in range(5): 49 | sweep_name = "sweep_%03i" % (i+1) 50 | ast.set_dataset("", times, name=sweep_name) 51 | 52 | 53 | # all done; close the file 54 | f.close() 55 | 56 | -------------------------------------------------------------------------------- /examples/create_scripts/annotations.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as ut 5 | 6 | 7 | """ 8 | Create and store experiment annotations 9 | 10 | Annotations are text strings that mark specific times in an 11 | experiment, for example "rat placed in enclosure" or "observed 12 | start of seizure activity". 13 | """ 14 | 15 | OUTPUT_DIR = "../created_nwb_files/" 16 | file_name = __file__[0:-3] + ".nwb" 17 | ######################################################################## 18 | # create a new NWB file 19 | # several settings are specified when doing so. these can be supplied within 20 | # the NWB constructor or defined in a dict, as in in this example 21 | settings = {} 22 | settings["file_name"] = OUTPUT_DIR + file_name 23 | 24 | # each file should have a descriptive globally unique identifier 25 | # that specifies the lab and this experiment session 26 | # the function nwb_utils.create_identifier() is recommended to use as it takes 27 | # the string and appends the present date and time 28 | settings["identifier"] = ut.create_identifier("annotation example") 29 | 30 | # indicate that it's OK to overwrite exting file 31 | settings["mode"] = "w" 32 | 33 | # specify the start time of the experiment. all times in the NWB file 34 | # are relative to experiment start time 35 | # if the start time is not specified the present time will be used 36 | 37 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 38 | # provide one or two sentences that describe the experiment and what 39 | # data is in the file 40 | settings["description"] = "Test file demonstrating use of the AbstractFeatureSeries" 41 | 42 | # create the NWB file object. this manages the file 43 | print("Creating " + settings["file_name"]) 44 | f = nwb_file.open(**settings) 45 | 46 | ######################################################################## 47 | # create an AnnotationSeries 48 | # this will be stored in 'acquisiiton' as annotations are an 49 | # observation or a record of something else that happened. 50 | # this means that it will be stored in the following location in the hdf5 51 | # file: acquisition/timeseries 52 | annot = f.make_group("", "notes", path="/acquisition/timeseries") 53 | annot.set_attr("description", "This is an AnnotationSeries with sample data") 54 | annot.set_attr("comments", "The comment and description fields can store arbitrary human-readable data") 55 | annot.set_attr("source", "Observation of Dr. J Doe") 56 | 57 | # store pretend data 58 | # all time is stored as seconds 59 | andata = [] 60 | andata.append(("Rat in bed, beginning sleep 1", 15.0)) 61 | andata.append(("Rat placed in enclosure, start run 1", 933.0)) 62 | andata.append(("Rat taken out of enclosure, end run 1", 1456.0)) 63 | andata.append(("Rat in bed, start sleep 2", 1461.0)) 64 | andata.append(("Rat placed in enclosure, start run 2", 2401.0)) 65 | andata.append(("Rat taken out of enclosure, end run 2", 3210.0)) 66 | andata.append(("Rat in bed, start sleep 3", 3218.0)) 67 | andata.append(("End sleep 3", 4193.0)) 68 | # convert the data to an array of annotations and times 69 | annotations = [x[0] for x in andata] 70 | times = [x[1] for x in andata] 71 | # store the annotations and times in the AnnotationSeries 72 | annot.set_dataset("data",annotations) 73 | annot.set_dataset("timestamps", times) 74 | 75 | # Ignore this block. these were used for testing external links 76 | # annot.set_dataset("data", "extlink:unknown_data_file,/path/to/data") 77 | # annot.set_dataset("timestamps", "extlink:unknown file2\t/path/t,o/timestamps") 78 | # num_samples must be explicitly set 79 | # annot.set_dataset("num_samples", 0) 80 | 81 | ######################################################################## 82 | # it can sometimes be useful to import documenting data from a file 83 | # in this case, we'll store this script in the metadata section of the 84 | # file, for a record of how the file was created 85 | 86 | script_name = sys.argv[0] 87 | f.set_dataset("source_script", ut.load_file(script_name), attrs= { 88 | "file_name": script_name}) 89 | 90 | # when all data is entered, close the file 91 | f.close() 92 | 93 | -------------------------------------------------------------------------------- /examples/create_scripts/behavior-e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as ut 5 | 6 | 7 | """ 8 | Store additional information (defined in an extension) in an Interface. 9 | 10 | This is the same as the behavior.py example, but adds a new dataset 11 | to the BehavioralEpochs, using an extension defined in file 12 | extensions/e-behavior.py. 13 | 14 | """ 15 | 16 | OUTPUT_DIR = "../created_nwb_files/" 17 | file_name = __file__[0:-3] + ".nwb" 18 | ######################################################################## 19 | # create a new NWB file 20 | settings = {} 21 | settings["file_name"] = OUTPUT_DIR + file_name 22 | settings["identifier"] = ut.create_identifier("behavioral interval example, with extension.") 23 | settings["mode"] = "w" 24 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 25 | settings["description"] = ("Test file demonstrating use of the BehavioralEpochs module " 26 | "interface with an extension") 27 | 28 | # specify the extension (Could be more than one. Only one used now). 29 | settings['extensions'] = ["extensions/e-behavior.py"] 30 | 31 | # create the NWB file object. this manages the file 32 | print("Creating " + settings["file_name"]) 33 | f = nwb_file.open(**settings) 34 | 35 | ######################################################################## 36 | # processed information is stored in modules, with each module publishing 37 | # one or more 'interfaces'. an interface is like a contract, promising 38 | # that the module will provide a specific and defined set of data. 39 | # this module will publish 'BehavioralEpochs' interface, which promises 40 | # that it will publish IntervalSeries (a type of time series storing 41 | # experimental intervals) 42 | # 43 | # create the module 44 | #- mod = neurodata.create_module("my behavioral module") 45 | mod = f.make_group("", "my behavioral module") 46 | mod.set_attr("description", "sample module that stores behavioral interval data") 47 | 48 | # add an interface 49 | if1 = mod.make_group("BehavioralEpochs") 50 | if1.set_attr("source", "a description of the original data that these intervals were calculated from ") 51 | 52 | # interval data is stored in an interval time series -- IntervalSeries 53 | # create it 54 | interval = if1.make_group("", "intervals") 55 | interval.set_attr("description", "Sample interval series -- two series are overlaid here, one with a code '1' and another with the code '2'") 56 | interval.set_attr("comments", "For example, '1' represents sound on(+1)/off(-1) and '2' represents light on(+2)/off(-2)") 57 | # create 58 | evts = [ 1, -1, 2, -2, 1, -1, 2, 1, -1, -2, 1, 2, -1, -2 ] 59 | interval.set_dataset("data", evts) 60 | 61 | # note: some timestamps will be duplicated if two different events start 62 | # and/or stop at the same time 63 | t = [ 1.0, 2.0, 2.0, 3.0, 5.0, 6.0, 6.0, 7.0, 8.0, 8.0, 10.0, 10.0, 11.0, 15.0 ] 64 | interval.set_dataset("timestamps", t) 65 | 66 | # Add additional information to the BehavioralEpochs interface. This is defined in 67 | # the extension "extensions/e-BehavioralEpochs.py" 68 | if1.set_dataset("my_extra_info", "extra info added to 'BehavioralEpochs' interface", 69 | attrs={"eia": "attribute for extra info"}) 70 | 71 | 72 | 73 | ######################################################################## 74 | # it can sometimes be useful to import documenting data from a file 75 | # in this case, we'll store this script in the metadata section of the 76 | # file, for a record of how the file was created 77 | script_name = sys.argv[0] 78 | f.set_dataset("source_script", ut.load_file(script_name), attrs= { 79 | "file_name": script_name}) 80 | 81 | # when all data is entered, close the file 82 | f.close() 83 | 84 | -------------------------------------------------------------------------------- /examples/create_scripts/closed_interface-e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as utils 5 | 6 | """ 7 | Example extending the format: using new Interface which is specified 8 | to be "closed" (does not allow any additional members). 9 | 10 | The extension is specified in file "extensions/e-closed_interface.py". 11 | 12 | The convention of having "e-" in front of the extension (and "-e" at the 13 | end of the create script name) is only used for these examples. Any name for the 14 | create script and extension(s) can be used as long as the actual name of the 15 | extension(s) are referenced by the create script and passed as parameters to 16 | nwb_validate.py when validating NWB files created using one or more extensions. 17 | 18 | 19 | """ 20 | # create a new NWB file 21 | OUTPUT_DIR = "../created_nwb_files/" 22 | file_name = __file__[0:-3] + ".nwb" 23 | 24 | settings = {} 25 | settings["file_name"] = OUTPUT_DIR + file_name 26 | settings["identifier"] = utils.create_identifier("MyClosedInterface example") 27 | settings["mode"] = "w" 28 | settings["start_time"] = "2016-04-07T03:16:03.604121" 29 | settings["description"] = "Test file demonstrating using a new Interface which is closed" 30 | 31 | # specify the extension 32 | settings['extensions'] = ["extensions/e-closed_interface.py"] 33 | f = nwb_file.open(**settings) 34 | 35 | 36 | ######################################################################## 37 | 38 | # create a module for the interface 39 | 40 | mod = f.make_group("", "my_module") 41 | 42 | # create the interface inside the module 43 | 44 | ig = mod.make_group("MyClosedInterface", attrs={"source": "source of data for MyClosedInterface"}) 45 | 46 | 47 | # set attribute and dataset in interface 48 | ig.set_attr("foo", "MyClosedInterface - foo attribute") 49 | ig.set_dataset("bar", [1, 2, 3, 4, 5]) 50 | 51 | # add an additional data set. This should generate an error on validation 52 | ig.set_custom_dataset("baz", [4, 6, 7, 9]) 53 | 54 | # All done. Close the file 55 | f.close() 56 | 57 | -------------------------------------------------------------------------------- /examples/create_scripts/custom_link.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as ut 5 | 6 | 7 | """ 8 | Test making a custom link to TimeSeries::data 9 | """ 10 | 11 | 12 | OUTPUT_DIR = "../created_nwb_files/" 13 | file_name = __file__[0:-3] + ".nwb" 14 | ######################################################################## 15 | # create a new NWB file 16 | # several settings are specified when doing so. these can be supplied within 17 | # the NWB constructor or defined in a dict, as in in this example 18 | settings = {} 19 | settings["file_name"] = OUTPUT_DIR + file_name 20 | settings["identifier"] = ut.create_identifier("custom link example") 21 | settings["mode"] = "w" 22 | settings["start_time"] = "Aug 24, 2016" 23 | settings["description"] = "Test creating custom link to TimeSeries::data" 24 | f = nwb_file.open(**settings) 25 | 26 | rss = f.make_group("", "rat_position", path='/acquisition/timeseries', 27 | attrs={"source": "optical sensor"}) 28 | rss_data = rss.set_dataset('data', [[1.1, 3.1], [1.2, 3.2], [1.3, 3.3]], attrs= { 29 | "conversion":1.0, "resolution":1.0, "unit":"meter"} ) 30 | rss.set_dataset('timestamps', [0.1, 0.2, 0.3]) 31 | 32 | # make custom group 33 | ag = f.make_group("analysis") 34 | cg = ag.make_custom_group("lab_data") 35 | ld = cg.set_custom_dataset("rat_position_data_link", rss_data) 36 | 37 | # Create another TimeSeries 38 | mss = f.make_group("", "mouse_position", path='/acquisition/timeseries', 39 | attrs={"source": "Differential GPS"}) 40 | mss_data = mss.set_dataset('data', [[7.1, 4.1], [7.2, 4.2], [7.3, 4.3]], attrs= { 41 | "conversion":1.0, "resolution":1.0, "unit":"meter"} ) 42 | mss.set_dataset('timestamps', [0.1, 0.2, 0.3]) 43 | # add a custom dataset in this timeseries to the other TimeSeries data array 44 | mss.set_custom_dataset("rat_position_data_link", rss_data) 45 | 46 | f.close() 47 | 48 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/0_README.txt: -------------------------------------------------------------------------------- 1 | This directory, "examples/scripts/extensions" will contain example 2 | extensions. Currently there is only one (e-interval.py) which is 3 | an extension that goes with the script "interval-e.py"). 4 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-analysis.py: -------------------------------------------------------------------------------- 1 | 2 | {"fs": {"aibs_ct_an": { 3 | 4 | 5 | "info": { 6 | "name": "AIBS cell types - analysis", 7 | "version": "0.9.2", 8 | "date": "May 6, 2016", 9 | "author": "Jeff Teeters, based on Allen Institute cell types DB HDF5 file", 10 | "contact": "jteeters@berkeley.edu", 11 | "description": "NWB extension for AIBS cell types data base NWB files /analysis section." 12 | }, 13 | 14 | "schema": { 15 | "/analysis/": { 16 | "aibs_spike_times/": { 17 | "description": "Group for storing AIBS specific spike times", 18 | "attributes": { 19 | "comments": { 20 | "data_type": "text", 21 | "value": "Spike times are relative to sweep start. The are NOT absolute times."} 22 | }, 23 | "": { 24 | "attributes": { 25 | "comments": { 26 | "data_type": "text", 27 | "value": "Spike times are relative to sweep start. The are NOT absolute times."} 28 | }, 29 | "description": "Times associated with a single sweep", 30 | "dimensions": ["numSamples"], 31 | "data_type": "float64!" 32 | } 33 | } 34 | } 35 | } 36 | 37 | }}} 38 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-behavior.py: -------------------------------------------------------------------------------- 1 | # Definitions of extension to BehavioralEpochs Interface 2 | 3 | 4 | # behei is the schema id (or 'namespace') 5 | 6 | {"fs": {"behei": { 7 | 8 | "info": { 9 | "name": "BehavioralEpochs extra info", 10 | "version": "1.0", 11 | "date": "May 6, 2016", 12 | "author": "Jeff Teeters", 13 | "contact": "jteeters@berkeley.edu", 14 | "description": ("Example extension to NWB BehavioralEpochs interface.") 15 | }, 16 | 17 | "schema": { 18 | "BehavioralEpochs/": { 19 | "description": "Extension to BehavioralEpochs interface to include a new dataset.", 20 | "my_extra_info": { 21 | "description": "dataset which contains extra info", 22 | "data_type": "text", 23 | "attributes": { 24 | "eia": { 25 | "description": "attribute for my_extra_info", 26 | "data_type": "text"}}} 27 | } 28 | } 29 | 30 | }}} -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-closed_interface.py: -------------------------------------------------------------------------------- 1 | # This defines a new interface, called MyClosedInterface 2 | # which is closed (does not allow new members to be added). 3 | 4 | # "eci" is the schema id for this extension. 5 | 6 | {"fs": { "eci": { 7 | 8 | "info": { 9 | "name": "Example closed Interface extension", 10 | "version": "1.0", 11 | "date": "Sept. 22, 2016", 12 | "author": "Jeff Teeters", 13 | "contact": "jteeters@berkeley.edu", 14 | "description": ("Extension defining a new closed Interface") 15 | }, 16 | 17 | "schema": { 18 | "MyClosedInterface/": { 19 | "merge": ["core:/"], 20 | "description": ("A new interface defined in extension e-closed-interface.py." 21 | " This is closed (no new members can be added)."), 22 | "_properties": {"closed": True}, # specify that this group is closed (no new members can be added). 23 | "attributes": { 24 | "foo": { 25 | "description": "example text attributed for MyClosedInterface", 26 | "data_type": "text"}}, 27 | "bar": { 28 | "description": ("Example dataset included with MyClosedInterface"), 29 | "data_type": "int", 30 | "dimensions": ["num_measurements"]}, 31 | "bazc/": { 32 | "description": ("Example closed group in MyClosedInterface"), 33 | # "_closed": True, 34 | "_properties": {"closed": True}}, 35 | "bazo/": { 36 | "description": ("Example open group in MyClosedInterface"), 37 | # "_closed": False, 38 | "_properties": {"closed": False}} 39 | } 40 | } 41 | 42 | }}} 43 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-genJson.py: -------------------------------------------------------------------------------- 1 | 2 | {"fs": {"genJson": { 3 | 4 | "info": { 5 | "name": "json storage extension", 6 | "version": "0.9.0", 7 | "date": "Oct 28, 2016", 8 | "author": "Jeff Teeters", 9 | "contact": "jteeters@berkeley.edu", 10 | "description": ("Extension for specifying storing of JSON formatted metadata in" 11 | " the general/json group.") 12 | }, 13 | 14 | "schema": { 15 | "/general/json/": { 16 | "description": "Location for storing JSON encoded metadata as text", 17 | "*": { 18 | "description": "Individual JSON file", 19 | "data_type": "text" 20 | } 21 | } 22 | } 23 | }}} 24 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-general.py: -------------------------------------------------------------------------------- 1 | 2 | # define an extension to add metadata to the /general section 3 | # 'rctn' is a key used to identify this extension 4 | # rctn stands for "Redwood Center for Theoretical Neuroscience" 5 | # (Any name could be used). 6 | 7 | 8 | {"fs": {"rctn": { 9 | 10 | "info": { 11 | "name": "RCTN extension", 12 | "version": "0.9.0", 13 | "date": "Feb 21, 2016", 14 | "author": "Jeff Teeters", 15 | "contact": "jteeters@berkeley.edu", 16 | "description": ("Redwood Center for Theoretical Neuroscience extension for the NWB" 17 | " format. Also includes some metadata for the AIBS cell types database") 18 | }, 19 | 20 | "schema": { 21 | '/general/activity_level': { 22 | 'data_type': 'text', 23 | 'description': "Activity level of animal. 10 - very active; 1-asleep"}, 24 | 'time_since_fed': { 25 | 'data_type': 'text', 26 | 'description': "Time animal last fed prior to session"}, 27 | "/general/": { 28 | "description": "Extension to core general", 29 | "include": { 'time_since_fed': {}}, 30 | "_required": { # Specifies required member combinations", 31 | "test_req" : 32 | ["notes AND experiment_description", 33 | "notes and experiment_description are both required"]}, 34 | "experimenter": { 35 | "attributes": { 36 | "orcid_id": { 37 | "description": "machine readable id, addeded with rctn schema", 38 | "data_type": "text"}}}, 39 | "rctn_info/": { 40 | "description": "Custom directory for rctn information", 41 | 'seminars': { 42 | "description": "Names of speakers in some past seminars", 43 | 'data_type': 'text', 44 | 'dimensions': ["num_seminars"]}, 45 | 'attendance': { 46 | "description": "Number of people attending corresponding seminar", 47 | 'data_type': 'int', 48 | 'dimensions': ["num_seminars"]}} 49 | }, 50 | # added metadata about the subject, from AIBS cell types database 51 | # 'aibs_' prefix was convention used in this instance but no particular naming 52 | # scheme is required 53 | "/general/subject/": { 54 | "aibs_specimen_id": { 55 | "data_type": "int", 56 | "description":"AIBS specific specimen ID"}, 57 | "aibs_specimen_name": { 58 | "data_type": "text", 59 | "description": "AIBS specific specimen_name"}, 60 | "aibs_dendrite_state": { 61 | "data_type": "text", 62 | "description": "AIBS specific dendrite_state"}, 63 | "aibs_dendrite_type": { 64 | "data_type": "text", 65 | "description": "AIBS specific dendrite type"}, 66 | "aibs_cre_line": { 67 | "data_type": "text", 68 | "description": "AIBS specific cre_line"} 69 | } 70 | } 71 | }}} -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-interface.py: -------------------------------------------------------------------------------- 1 | # Definitions of an extension defining a new interface 2 | 3 | # This defines a new interface, called MyNewInterface 4 | # All format specifications must be stored in dictionary "fs" 5 | 6 | # "eint" is the schema id (or namespace) for this extension. 7 | 8 | {"fs": { "eint": { 9 | 10 | "info": { 11 | "name": "Example Interface extension", 12 | "version": "1.0", 13 | "date": "May 2, 2016", 14 | "author": "Jeff Teeters", 15 | "contact": "jteeters@berkeley.edu", 16 | "description": ("Extension defining a new Interface type, named 'MyNewInterface'") 17 | }, 18 | 19 | "schema": { 20 | "MyNewInterface/": { 21 | "merge": ["core:/"], 22 | "description": ("A new interface defined in extension e-interface.py. Uses the " 23 | "new timeseries defined in extension e-timeseries.py"), 24 | "attributes": { 25 | "foo": { 26 | "description": "example text attributed for MyNewInterface", 27 | "data_type": "text"}}, 28 | "/": { 29 | # use MyNewTimeSeries in the MyNewInterface 30 | "merge": ["mnts:/"] 31 | }, 32 | "bar": { 33 | "description": ("Example dataset included with MyNewTimeSeries"), 34 | "data_type": "int", 35 | "dimensions": ["num_measurements"]} 36 | } 37 | } 38 | 39 | }}} 40 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-interval.py: -------------------------------------------------------------------------------- 1 | # Definitions of extension to IntervalSeries 2 | 3 | # "isc" is the schema id (or 'namespace') 4 | # "fs" must always be the top level key 5 | 6 | {"fs": {"isc": { 7 | 8 | "info": { 9 | "name": "Interval series code descriptions", 10 | "version": "1.0", 11 | "date": "April 7, 2016", 12 | "author": "Jeff Teeters", 13 | "contact": "jteeters@berkeley.edu", 14 | "description": ("Extension to NWB Interval Series to include a code and " 15 | "code_description dataset.") 16 | }, 17 | 18 | "schema": { 19 | "/": { 20 | "description": "Extension to IntervalSeries to include code descriptions.", 21 | "codes": { 22 | "description": "Codes that are used in the IntervalSeries", 23 | "data_type": "int", 24 | "dimensions": ["num_codes"] }, 25 | "code_descriptions": { 26 | "description": "Description of each code", 27 | "data_type": "text", 28 | "dimensions": ["num_codes"] }} 29 | } 30 | 31 | }}} 32 | 33 | 34 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-intracellular.py: -------------------------------------------------------------------------------- 1 | # Definitions of AIBS cell types extension to NWB format 2 | 3 | {"fs": {"aibs_ct_intra": { 4 | 5 | "info": { 6 | "name": "AIBS Cell Types - intracellular metadata", 7 | "version": "0.9.3", 8 | "date": "Oct 3, 2016", 9 | "author": "Jeff Teeters, based on HDF5 created by Keith Godfrey using AIBS NWB API", 10 | "contact": "jteeters@berkeley.edu", 11 | "description": "NWB extension for intracellular metadata base onf AIBS cell types data base NWB files." 12 | }, 13 | 14 | "schema": { 15 | "/": { 16 | "description": ("AIBS specific VoltageClampSeries. Includes AIBS sepcific metadata."), 17 | "aibs_stimulus_amplitude_mv": { 18 | "description": "AIBS specific stimulus_amplitude", 19 | "attributes": { 20 | "unit": { "data_type": "text", "value": "mv"}}, 21 | "data_type": "float"}, 22 | "aibs_stimulus_description": { 23 | "description": "AIBS specific stimulus description", 24 | "data_type": "text"}, 25 | "aibs_stimulus_interval": { 26 | "description": "AIBS specific stimulus interval", 27 | "data_type": "float"}, 28 | "aibs_stimulus_name": { 29 | "description": "AIBS specific stimulus name", 30 | "data_type": "text"}, 31 | }, 32 | "/": { 33 | "description": ("AIBS specific CurrentClampSeries. Includes AIBS sepcific metadata."), 34 | "aibs_stimulus_amplitude_pa": { 35 | "description": "AIBS specific stimulus_amplitude", 36 | "attributes": { 37 | "unit": { "data_type": "text", "value": "pa"}}, 38 | "data_type": "float"}, 39 | "aibs_stimulus_description": { 40 | "description": "AIBS specific stimulus description", 41 | "data_type": "text"}, 42 | "aibs_stimulus_interval": { 43 | "description": "AIBS specific stimulus interval", 44 | "data_type": "float"}, 45 | "aibs_stimulus_name": { 46 | "description": "AIBS specific stimulus name", 47 | "data_type": "text"}, 48 | }, 49 | "/stimulus/presentation//": { 50 | "description": ("AIBS specific CurrentClampStimulusSeries, only applies to " 51 | "location /stimulus/presentation/, but not to location /stimulus/templates"), 52 | "aibs_stimulus_amplitude_pa": { 53 | "description": "AIBS specific stimulus_amplitude", 54 | "attributes": { 55 | "unit": { "data_type": "text", "value": "mv"}}, 56 | "data_type": "float"}, 57 | "aibs_stimulus_description": { 58 | "description": "AIBS specific stimulus description", 59 | "data_type": "text"}, 60 | "aibs_stimulus_interval": { 61 | "description": "AIBS specific stimulus interval", 62 | "data_type": "float"}, 63 | "aibs_stimulus_name": { 64 | "description": "AIBS specific stimulus name", 65 | "data_type": "text"}, 66 | }, 67 | "/stimulus/presentation//": { 68 | "description": ("AIBS specific VoltageClampStimulusSeries, only applies to " 69 | "location /stimulus/presentation/, not to location /stimulus/templates"), 70 | "aibs_stimulus_amplitude_mv": { 71 | "description": "AIBS specific stimulus_amplitude", 72 | "attributes": { 73 | "unit": { "data_type": "text", "value": "mv"}}, 74 | "data_type": "float"}, 75 | "aibs_stimulus_description": { 76 | "description": "AIBS specific stimulus description", 77 | "data_type": "text"}, 78 | "aibs_stimulus_interval": { 79 | "description": "AIBS specific stimulus interval", 80 | "data_type": "float"}, 81 | "aibs_stimulus_name": { 82 | "description": "AIBS specific stimulus name", 83 | "data_type": "text"}, 84 | } 85 | } 86 | 87 | }}} -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-link_test.py: -------------------------------------------------------------------------------- 1 | 2 | {"fs": {"link_test": { 3 | 4 | 5 | "info": { 6 | "name": "link_test", 7 | "version": "0.1", 8 | "date": "May 6, 2016", 9 | "author": "Jeff Teeters", 10 | "contact": "jteeters@berkeley.edu", 11 | "description": "Test defining a link in an extension to debug schema_id." 12 | }, 13 | 14 | "schema": { 15 | "/analysis/": { 16 | "aibs_spike_times/": { 17 | "description": "Group for storing AIBS specific spike times", 18 | "pto_link?": { 19 | "description": ("The offset from the frame timestamp at which each pixel was acquired." 20 | " Note that the offset is not time-varying, i.e. it is the same for" 21 | " each frame. These offsets are given in the same units as for the" 22 | " timestamps array, i.e. seconds."), 23 | "link": {"target_type": "pixel_time_offsets", 24 | # "allow_subclasses": False # allow_subclasses not allowed in dataset links 25 | }, 26 | "data_type": "float64!" 27 | }, 28 | "pixel_time_offsets": { 29 | "description": ("The offset from the frame timestamp at which each pixel in this ROI" 30 | " was acquired." 31 | " Note that the offset is not time-varying, i.e. it is the same for" 32 | " each frame. These offsets are given in the same units as for the" 33 | " timestamps array, i.e. seconds."), 34 | "data_type": "float64!", 35 | "dimensions": [["y"], ["y", "x"]] 36 | } 37 | } 38 | } 39 | } 40 | 41 | }}} 42 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-module.py: -------------------------------------------------------------------------------- 1 | # Definitions of an extension defining a custom module 2 | 3 | # In the NWB core format, each module can contain any number of interfaces 4 | # and no particular interfaces are required. 5 | 6 | # This extension shows how to create a custom module that specifies that 7 | # two interfaces are required. The two interfaces required are a custom 8 | # interface named "MyNewInterface" and the BehavioralTimeSeries interface. 9 | 10 | # The custom module is named "" 11 | 12 | # All format specifications must be stored in dictionary "fs" 13 | 14 | # "eint" is the schema id (or namespace) for this extension. 15 | 16 | {"fs": { "new_mod": { 17 | 18 | 19 | "info": { 20 | "name": "Example custom module extension", 21 | "version": "1.0", 22 | "date": "Sept. 22, 2016", 23 | "author": "Jeff Teeters", 24 | "contact": "jteeters@berkeley.edu", 25 | "description": ("Extension defining a new Module type, named 'MyNewModule', that has" 26 | " two required interfaces") 27 | }, 28 | 29 | "schema": { 30 | "/": { 31 | "merge": ["core:/"], 32 | "description": ("A new module defined in extension e-module.py. Requires two " 33 | "Interfaces (MyNewInterface and BehavioralTimeSeries)."), 34 | "include": { 35 | "eint:MyNewInterface/": {}, 36 | "core:BehavioralTimeSeries/": {} }} 37 | } 38 | }}} 39 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-timeseries.py: -------------------------------------------------------------------------------- 1 | # Example extension defining a new TimeSeries 2 | 3 | # All format specifications must be stored in dictionary with top level key "fs": 4 | # "mnts" is the "namespace" for this extension. 5 | 6 | 7 | {"fs": {"mnts": { 8 | "info": { 9 | "name": "Example TimeSeries extension", 10 | "version": "1.0", 11 | "date": "May 2, 2016", 12 | "author": "Jeff Teeters", 13 | "contact": "jteeters@berkeley.edu", 14 | "description": ("Extension defining a new TimeSeries type, named 'MyNewTimeSeries'") 15 | }, 16 | 17 | "schema": { 18 | "/": { 19 | "description": "A new timeseries, defined in extension e-timeseries.py", 20 | "merge": ["core:/"], 21 | "attributes": { 22 | "ancestry": { 23 | "data_type": "text", 24 | "dimensions": ["2"], 25 | "value": ["TimeSeries", "MyNewTimeSeries"], 26 | "const": True}, 27 | "help": { 28 | "data_type": "text", 29 | "value": "Short description of MyNewTimeSeries goes here", 30 | "const": True}, 31 | "foo": { 32 | "description": "example new text attributed for MyNewTimeSeries", 33 | "data_type": "text"}}, 34 | "data": { 35 | "description": ("Multiple measurements are recorded at each point of time."), 36 | "dimensions": ["num_times", "num_measurements"], 37 | "data_type": "float32"}, 38 | "bar": { 39 | "description": ("Example dataset included with MyNewTimeSeries"), 40 | "data_type": "int", 41 | "dimensions": ["num_measurements"]} 42 | } 43 | } 44 | }}} 45 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-trajectorySeries.py: -------------------------------------------------------------------------------- 1 | # Definitions of extension to TimeSeries to store trajectory information 2 | # All format specifications must be stored in dictionary "fs": 3 | # "mnts" is the schema id or "namespace" for this extension. 4 | 5 | {"fs": {"mnts": { 6 | 7 | "info": { 8 | "name": "Sabes lab data trajectory series", 9 | "version": "1.0", 10 | "date": "May 2, 2016", 11 | "author": "Jeff Teeters", 12 | "contact": "jteeters@berkeley.edu", 13 | "description": ("Extension to store timeseries of hand trajectories for Sabes lab data") 14 | }, 15 | 16 | "schema": { 17 | "/": { 18 | "merge": ["core:/"], 19 | "attributes": { 20 | "ancestry": { 21 | "data_type": "text", 22 | "dimensions": ["2"], 23 | "value": ["TimeSeries", "TrajectorySeries"], 24 | "const": True}, 25 | "help": { 26 | "data_type": "text", 27 | "value": "Trajectory of hand movement positions", 28 | "const": True}, 29 | "measurement_names": { 30 | "description": "Names of measurements at each time point", 31 | "data_type": "text", 32 | "dimensions": ["num_measurements"]}, 33 | "measurement_units": { 34 | "description": "Units of each measurement", 35 | "data_type": "text", 36 | "dimensions": ["num_measurements"]}, 37 | }, 38 | "data": { 39 | "description": ("Measurements of hand trajectory, recorded at each point of time."), 40 | "dimensions": ["num_times", "num_measurements"], 41 | "data_type": "float32"}, 42 | } 43 | } 44 | 45 | }}} 46 | -------------------------------------------------------------------------------- /examples/create_scripts/extensions/e-trajectorySeries2.py: -------------------------------------------------------------------------------- 1 | # Definitions of extension to TimeSeries to store trajectory information 2 | # All format specifications must be stored in dictionary "fs" 3 | # "mnts2" is the "namespace" for this extension 4 | # This extension explicitly specifies meaning for each column of dataset data 5 | 6 | {"fs": {"mnts2": { 7 | 8 | "info": { 9 | "name": "Sabes lab data trajectory series", 10 | "version": "1.0", 11 | "date": "Oct 3, 2016", 12 | "author": "Jeff Teeters", 13 | "contact": "jteeters@berkeley.edu", 14 | "description": ("Extension to store timeseries of hand trajectories for Sabes lab data") 15 | }, 16 | 17 | "schema": { 18 | "/": { 19 | "merge": ["core:/"], 20 | "attributes": { 21 | "ancestry": { 22 | "data_type": "text", 23 | "dimensions": ["3"], 24 | "value": ["TimeSeries", "SpatialSeries", "TrajectorySeries"], 25 | "const": True}, 26 | "help": { 27 | "data_type": "text", 28 | "value": "Trajectory of hand movement positions", 29 | "const": True}, 30 | }, 31 | "data": { 32 | "description": ("Measurements of hand trajectory, recorded at each point of time."), 33 | "dimensions": ["num_times", "trajectories"], 34 | "data_type": "float32", 35 | "trajectories": { 36 | "type": "structure", 37 | # define components of trajectories dimension 38 | "components": [ 39 | { "alias": "s1_x", "unit": "meter" }, 40 | { "alias": "s1_y", "unit": "meter" }, 41 | { "alias": "s1_z", "unit": "meter" }, 42 | { "alias": "s1_pitch", "unit": "radian" }, 43 | { "alias": "s1_roll", "unit": "radian" }, 44 | { "alias": "s1_yaw", "unit": "radian" }, 45 | { "alias": "s2_x", "unit": "meter" }, 46 | { "alias": "s2_y", "unit": "meter" }, 47 | { "alias": "s2_z", "unit": "meter" }, 48 | { "alias": "s2_pitch", "unit": "radian" }, 49 | { "alias": "s2_roll", "unit": "radian" }, 50 | { "alias": "s2_yaw", "unit": "radian" }, 51 | { "alias": "s3_x", "unit": "meter" }, 52 | { "alias": "s3_y", "unit": "meter" }, 53 | { "alias": "s3_z", "unit": "meter" }, 54 | { "alias": "s3_pitch", "unit": "radian" }, 55 | { "alias": "s3_roll", "unit": "radian" }, 56 | { "alias": "s3_yaw", "unit": "radian" }, 57 | { "alias": "s4_x", "unit": "meter" }, 58 | { "alias": "s4_y", "unit": "meter" }, 59 | { "alias": "s4_z", "unit": "meter" }, 60 | { "alias": "s4_pitch", "unit": "radian" }, 61 | { "alias": "s4_roll", "unit": "radian" }, 62 | { "alias": "s4_yaw", "unit": "radian" } ] }, 63 | } 64 | } 65 | } 66 | 67 | }}} -------------------------------------------------------------------------------- /examples/create_scripts/general-e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as utils 5 | 6 | """ 7 | Example using extension to add metadata to group /general 8 | 9 | Group /general contains general metadata, i.e. metadata that 10 | applies to the entire session. 11 | 12 | This example uses the extension defined in extensions/e-general.py 13 | to add new metadata to define then add new metadata to section 14 | /general 15 | 16 | """ 17 | # create a new NWB file 18 | OUTPUT_DIR = "../created_nwb_files/" 19 | file_name = __file__[0:-3] + ".nwb" 20 | 21 | settings = {} 22 | settings["file_name"] = OUTPUT_DIR + file_name 23 | settings["identifier"] = utils.create_identifier("add metadata to general") 24 | settings["mode"] = "w" 25 | settings["start_time"] = "2016-04-07T03:16:03.604121" 26 | settings["description"] = "Test file demonstrating use of an extension for general" 27 | 28 | # specify the extension (Could be more than one. Only one used now). 29 | settings['extensions'] = ["extensions/e-general.py"] 30 | f = nwb_file.open(**settings) 31 | 32 | 33 | ######################################################################## 34 | # Specifier experimenter (this dataset is part of the core NWB format) 35 | eds = f.set_dataset('experimenter', "Joseline Doe") 36 | 37 | # specify attribute to experimenter, this defined in extension file. 38 | # it is not part of the core NWB format 39 | eds.set_attr("orcid_id", "7012023") 40 | 41 | # Now add metadata that is defined by the extension 42 | gri = f.make_group("rctn_info") 43 | gri.set_dataset("seminars", ["Thom Smith", "Dwight Keenan", "Sue Trimble"]) 44 | gri.set_dataset("attendance", [23, 45, 33]) 45 | f.set_dataset("rctn:activity_level", '7') 46 | f.set_dataset("rctn:time_since_fed", '6 hours 20 minutes') 47 | 48 | f.set_dataset("notes", "some notes") 49 | 50 | # also set extra metadata about subject 51 | # these datasets are also defined in the extension 52 | # dataset names and values are from a file in the AIBS cell types database 53 | f.set_dataset("aibs_specimen_id",313862134) 54 | f.set_dataset("aibs_specimen_name","Sst-IRES-Cre;Ai14(IVSCC)-167638.03.01.01") 55 | f.set_dataset("aibs_dendrite_state","NA") 56 | f.set_dataset("aibs_dendrite_type","aspiny") 57 | f.set_dataset("aibs_cre_line","Sst-IRES-Cre") 58 | 59 | # All done. Close the file 60 | f.close() 61 | 62 | -------------------------------------------------------------------------------- /examples/create_scripts/interface-e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as utils 5 | 6 | """ 7 | Example extending the format: creating a new Interface. 8 | 9 | This example uses two extensions defined in director "extensions" 10 | e-interface.py - defines Interface extension 11 | e-timeseries.py - defines a new timeseries type (MyNewTimeSeries) 12 | 13 | The convention of having "e-" in front of the extension (and "-e" at the 14 | end of the create script name) is only used for these examples. Any name for the 15 | create script and extension(s) can be used as long as the actual name of the 16 | extension(s) are referenced by the create script and passed as parameters to 17 | nwb_validate.py when validating NWB files created using one or more extensions. 18 | 19 | 20 | """ 21 | # create a new NWB file 22 | OUTPUT_DIR = "../created_nwb_files/" 23 | file_name = __file__[0:-3] + ".nwb" 24 | 25 | settings = {} 26 | settings["file_name"] = OUTPUT_DIR + file_name 27 | settings["identifier"] = utils.create_identifier("MyNewInterface example") 28 | settings["mode"] = "w" 29 | settings["start_time"] = "2016-04-07T03:16:03.604121" 30 | settings["description"] = "Test file demonstrating using a new Interface type using an extension" 31 | 32 | # specify the extensions, two are used. 33 | settings['extensions'] = ["extensions/e-timeseries.py", "extensions/e-interface.py"] 34 | f = nwb_file.open(**settings) 35 | 36 | 37 | ######################################################################## 38 | 39 | # create a module for the interface 40 | 41 | mod = f.make_group("", "my_module") 42 | 43 | # create the interface inside the module 44 | 45 | ig = mod.make_group("MyNewInterface", attrs={"source": "source of data for MyNewInterface"}) 46 | 47 | 48 | # set attribute and dataset in interface 49 | ig.set_attr("foo", "MyNewInterface - foo attribute") 50 | ig.set_dataset("bar", [1, 2, 3, 4, 5]) 51 | 52 | 53 | # Make some sample data for the MyNewTimeseries 54 | 55 | data = [[1.2, 1.3, 1.4], [2.2, 2.3, 2.4], [3.2, 3.3, 3.4], [4.2, 4.3, 4.4], [5.2, 5.3, 5.4]] 56 | times = [0.1, 0.2, 0.3, 0.4, 0.5] 57 | 58 | # create the MyNewtimeseries inside the interface 59 | nts = ig.make_group("", "my_new_ts", attrs={"source": "source of data for my_new_ts"}) 60 | 61 | nts.set_dataset("data", data, attrs={"conversion": 1.0, "resolution": 0.001, "unit": "--unit goes here--"}) 62 | nts.set_dataset("timestamps", times) 63 | 64 | # specify metadata that is part of MyNewTimeSeries type 65 | nts.set_attr("foo", "This added to attribute 'foo'") 66 | nts.set_dataset("bar", [2, 4, 5, 6, 7]) 67 | 68 | # All done. Close the file 69 | f.close() 70 | 71 | -------------------------------------------------------------------------------- /examples/create_scripts/interval-e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as utils 5 | 6 | """ 7 | Create and store interval series 8 | 9 | This is the same as example: interval.py, except that it uses 10 | and extension (defined in extensions/e-interval.py) to add 11 | a two new datasets: 12 | - "codes" 13 | - "code_descriptions" 14 | to the IntervalSeries. The codes data set lists the numeric codes used. 15 | The "code_descriptions" data set, provides the description of each code. 16 | """ 17 | # create a new NWB file 18 | OUTPUT_DIR = "../created_nwb_files/" 19 | file_name = __file__[0:-3] + ".nwb" 20 | 21 | settings = {} 22 | settings["file_name"] = OUTPUT_DIR + file_name 23 | settings["identifier"] = utils.create_identifier("extended interval example") 24 | settings["mode"] = "w" 25 | settings["start_time"] = "2016-04-07T03:16:03.604121" 26 | settings["description"] = "Test file demonstrating use of an extended IntervalSeries" 27 | 28 | # specify the extension (Could be more than one. Only one used now). 29 | settings['extensions'] = ["extensions/e-interval.py"] 30 | f = nwb_file.open(**settings) 31 | 32 | 33 | ######################################################################## 34 | # Make some fake interval series data 35 | # store in codes and times 36 | event_codes = [ 37 | 7, # 300 hz tone turned on at 38 | -7, # 300 hz tone turned off 39 | 3, # blue light turned on 40 | 4, # 200 hz tone turned on 41 | 6, # red light turned on 42 | -3, # blue light turned off 43 | -6, # red light turned off 44 | -4 # 200 hz tone turned off 45 | ] 46 | # times - interval times (in seconds) corresponding to above codes 47 | event_times = [1.1, 2.3, 3.3, 4.4, 5.5, 6.6, 7.7, 8.8] 48 | 49 | # create two arrays, one containing the codes, the other the corresponding 50 | # descriptions 51 | codes = [3, 4, 6, 7] 52 | code_descriptions = ["blue light", "200 hz tone", "red light", "300 hz tone"] 53 | 54 | 55 | ######################################################################## 56 | # create an IntervalSeries 57 | # All time series created at the "top level" in the file (e.g. not inside 58 | # a defined structure in the format specification) are stored in 59 | # one of three locations: 60 | # /stimulus/presentation - for presented stimuli data 61 | # /stimulus/templates - for templates for stimuli 62 | # /acquisition/timeseries - for acquired data 63 | # 64 | # Store this interval series in /stimulus/presentation 65 | # that is specified by the 'path' parameter in the call below 66 | 67 | # create the group for the IntervalSeries. Call returns group object 68 | g = f.make_group("", "tone_times", path="/stimulus/presentation") 69 | 70 | # # Inside the group, create the data and timestamps datasets 71 | g.set_dataset("data", event_codes) 72 | g.set_dataset("timestamps", event_times) 73 | 74 | # Now add the data sets defined in the extension 75 | g.set_dataset("codes", codes) 76 | g.set_dataset("code_descriptions", code_descriptions) 77 | 78 | 79 | # All done. Close the file 80 | f.close() 81 | 82 | -------------------------------------------------------------------------------- /examples/create_scripts/interval.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as ut 5 | 6 | """ 7 | Create and store interval series 8 | 9 | Intervals in the data can be efficiently stored using the NWB IntervalSeries. 10 | 11 | The timestamps field stores the beginning and end of intervals. 12 | The data field stores whether the interval just started (>0 value) 13 | or ended (<0 value). Different interval types can be represented in the 14 | same series by using multiple key values (eg, 1 for feature A, 15 | 2 for feature B, 3 for feature C, etc). The field data stores an 8-bit integer. 16 | This is largely an alias of a standard TimeSeries but that is identifiable as 17 | representing time intervals in a machine-readable way. 18 | """ 19 | 20 | # create a new NWB file 21 | OUTPUT_DIR = "../created_nwb_files/" 22 | file_name = __file__[0:-3] + ".nwb" 23 | settings = {} 24 | settings["file_name"] = OUTPUT_DIR + file_name 25 | settings["identifier"] = ut.create_identifier("interval example") 26 | settings["mode"] = "w" 27 | settings["start_time"] = "2016-04-07T03:16:03.604121" 28 | settings["description"] = "Test file demonstrating use of the IntervalSeries" 29 | f = nwb_file.open(**settings) 30 | 31 | 32 | ######################################################################## 33 | # Make some fake interval series data 34 | # store in codes and times 35 | event_codes = [ 36 | 7, # 300 hz tone turned on 37 | -7, # 300 hz tone turned off 38 | 3, # blue light turned on 39 | 4, # 200 hz tone turned on 40 | 6, # red light turned on 41 | -3, # blue light turned off 42 | -6, # red light turned off 43 | -4 # 200 hz tone turned off 44 | ] 45 | # times - interval times (in seconds) corresponding to above codes 46 | event_times = [1.1, 2.3, 3.3, 4.4, 5.5, 6.6, 7.7, 8.8] 47 | 48 | ######################################################################## 49 | # create an IntervalSeries 50 | # All time series created at the "top level" in the file (e.g. not inside 51 | # a defined structure in the format specification) are stored in 52 | # one of three locations: 53 | # /stimulus/presentation - for presented stimuli data 54 | # /stimulus/templates - for templates for stimuli 55 | # /acquisition/timeseries - for acquired data 56 | # 57 | # Store this interval series in /stimulus/presentation 58 | # that is specified by the 'path' parameter in the call below 59 | 60 | # create the group for the IntervalSeries. Call returns group object 61 | g = f.make_group("", "tone_times", path="/stimulus/presentation") 62 | g.set_attr("description", "Times for tone turning on/off. data codes positive for on, negative for off") 63 | 64 | # # Inside the group, create the data and timestamps datasets 65 | g.set_dataset("data", event_codes) 66 | g.set_dataset("timestamps", event_times) 67 | 68 | 69 | # All done. Close the file 70 | f.close() 71 | 72 | -------------------------------------------------------------------------------- /examples/create_scripts/link_test-e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as ut 5 | 6 | 7 | """ 8 | Test extension defining a link 9 | 10 | """ 11 | 12 | OUTPUT_DIR = "../created_nwb_files/" 13 | file_name = __file__[0:-3] + ".nwb" 14 | ######################################################################## 15 | # create a new NWB file 16 | settings = {} 17 | settings["file_name"] = OUTPUT_DIR + file_name 18 | settings["identifier"] = ut.create_identifier("test link extension.") 19 | settings["mode"] = "w" 20 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 21 | settings["description"] = ("Test making a link in the /analysis group " 22 | "that is defined by an extension.") 23 | 24 | # specify the extension (Could be more than one. Only one used now). 25 | settings['extensions'] = ["extensions/e-link_test.py"] 26 | 27 | # create the NWB file object. this manages the file 28 | print("Creating " + settings["file_name"]) 29 | f = nwb_file.open(**settings) 30 | 31 | ######################################################################## 32 | # This example, stores spike times for multiple sweeps 33 | # create the group for the spike times 34 | # The group ("aibs_spike_times") is defined in the extension 35 | 36 | ast = f.make_group("aibs_spike_times") 37 | 38 | # some sample data 39 | times = [1.1, 1.2, 1.3, 1.4, 1.5] 40 | 41 | # 42 | pto = ast.set_dataset("pixel_time_offsets", times) 43 | 44 | # now make the link 45 | ptl = ast.set_dataset("pto_link", pto, attrs={"hello": "Natasha"}) 46 | ptl.set_attr("Mary", "bendrich") 47 | 48 | # all done; close the file 49 | f.close() 50 | 51 | -------------------------------------------------------------------------------- /examples/create_scripts/module-e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as utils 5 | 6 | """ 7 | Example extending the format: creating a module with required interfaces. 8 | 9 | In the NWB core format, each module can contain any number of interfaces 10 | and no particular interfaces are required. 11 | 12 | This example shows using a custom module that specifies that two interfaces 13 | are required, a custom interface named "MyNewInterface" and the 14 | BehavioralTimeSeries interface. 15 | 16 | This example uses two extensions defined in director "extensions" 17 | e-module.py - defines the custom module 18 | e-interface.py - defines Interface extension 19 | e-timeseries.py - defines a new TimeSeries type (MyNewTimeSeries) 20 | 21 | The convention of having "e-" in front of the extension (and "-e" at the 22 | end of the create script name) is only used for these examples. Any name for the 23 | create script and extension(s) can be used as long as the actual name of the 24 | extension(s) are referenced by the create script and passed as parameters to 25 | nwb_validate.py when validating NWB files created using one or more extensions. 26 | 27 | 28 | """ 29 | # create a new NWB file 30 | OUTPUT_DIR = "../created_nwb_files/" 31 | file_name = __file__[0:-3] + ".nwb" 32 | 33 | settings = {} 34 | settings["file_name"] = OUTPUT_DIR + file_name 35 | settings["identifier"] = utils.create_identifier("Custom module example") 36 | settings["mode"] = "w" 37 | settings["start_time"] = "2016-04-07T03:16:03.604121" 38 | settings["description"] = "Test file demonstrating using a custom module using an extension" 39 | 40 | # specify the extensions, two are used. 41 | settings['extensions'] = ["extensions/e-timeseries.py", 42 | "extensions/e-interface.py", "extensions/e-module.py"] 43 | f = nwb_file.open(**settings) 44 | 45 | 46 | ######################################################################## 47 | 48 | # create a module for the interface 49 | mod = f.make_group("new_mod:", "custom_module") 50 | 51 | # create the interface inside the module 52 | ig = mod.make_group("MyNewInterface", attrs={"source": "source of data for MyNewInterface"}) 53 | 54 | # set attribute and dataset in interface 55 | ig.set_attr("foo", "MyNewInterface - foo attribute") 56 | ig.set_dataset("bar", [1, 2, 3, 4, 5]) 57 | 58 | 59 | # Make some sample data for the MyNewTimeseries 60 | data = [[1.2, 1.3, 1.4], [2.2, 2.3, 2.4], [3.2, 3.3, 3.4], [4.2, 4.3, 4.4], [5.2, 5.3, 5.4]] 61 | times = [0.1, 0.2, 0.3, 0.4, 0.5] 62 | 63 | # create the MyNewtimeseries inside the interface 64 | nts = ig.make_group("", "my_new_ts", attrs={"source": "source of data for my_new_ts"}) 65 | 66 | nts.set_dataset("data", data, attrs={"conversion": 1.0, "resolution": 0.001, "unit": "--unit goes here--"}) 67 | nts.set_dataset("timestamps", times) 68 | 69 | # specify metadata that is part of MyNewTimeSeries type 70 | nts.set_attr("foo", "This added to attribute 'foo'") 71 | nts.set_dataset("bar", [2, 4, 5, 6, 7]) 72 | 73 | # add the behavioral timeseries to the module 74 | 75 | ib = mod.make_group("BehavioralTimeSeries", attrs={"source": "source of data for BehavioralTimeSeries"}) 76 | 77 | ts1 = ib.make_group("", "rat_position", attrs={"source": "source of data for rat_position"}) 78 | ts1.set_dataset("data", data, attrs={"conversion": 1.0, "resolution": 0.001, "unit": "--unit goes here--"}) 79 | ts1.set_dataset("timestamps", times) 80 | 81 | # All done. Close the file 82 | f.close() 83 | 84 | -------------------------------------------------------------------------------- /examples/create_scripts/run_all.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # This script will run all the example create scripts. 4 | # 5 | # It is run by entering the script name, optionally followed by character "s" or "f". 6 | # "s" specifies text output should be displayed on the screen, "f" indicates the 7 | # text output should be sent to a file, in directory "../text_output_files/create". 8 | # Writing to a file is useful for comparing the text output of each 9 | # create script to the output of validating the created nwb file. 10 | # (The output from both should be mostly the same) and to the output generated 11 | # in other runs. The output is used by the scripts in the "test_all" directory 12 | # at the top level. 13 | # The 'validate_all.py' script (in directory '../utility_scripts') can be used 14 | # to validate all the NWB files created by these scripts. 15 | 16 | txt_output_dir="../text_output_files/create" 17 | nwb_output_dir="../created_nwb_files" 18 | 19 | output_mode=$1 20 | if [[ "$output_mode" == "" ]] ; then 21 | output_mode="f" 22 | fi 23 | 24 | if [[ ! "$output_mode" =~ [fs]$ ]] ; then 25 | echo "format is:" 26 | echo "$0 " 27 | echo "where, is one of:" 28 | echo " f - output to file in $txt_output_dir" 29 | echo " s - output to screen." 30 | echo " default is 'f'" 31 | exit 1 32 | fi 33 | if [[ "$output_mode" == 's' ]] ; then 34 | dest="screen" 35 | else 36 | dest="directory $txt_output_dir" 37 | fi 38 | 39 | source_data_dir="source_data_2" 40 | source_data_test_file="../$source_data_dir/crcns_alm-1/data_collection.txt" 41 | 42 | if [[ -f "$source_data_test_file" ]] ; then 43 | have_source_data="1" 44 | source_data_msg="Have ../$source_data_dir directory contents, running scripts that use it." 45 | else 46 | have_source_data="0" 47 | source_data_msg="Did not find ./$source_data_dir directory contents. Skipping scripts that use it." 48 | fi 49 | 50 | echo "sending output to $dest" 51 | echo "$source_data_msg" 52 | 53 | 54 | if [[ "$output_mode" == 'f' ]] ; then 55 | # make sure text output directory exists and is empty 56 | if [[ ! -d "$txt_output_dir" ]]; then 57 | mkdir $txt_output_dir 58 | echo "created $txt_output_dir" 59 | else 60 | rm -f $txt_output_dir/*.txt 61 | echo "cleared $txt_output_dir" 62 | fi 63 | fi 64 | 65 | 66 | 67 | function run_script { 68 | script=$1 69 | if [[ "$output_mode" == "f" ]] ; then 70 | stem=${script%.*} 71 | output_file="$stem.txt" 72 | echo "doing 'python $script > $txt_output_dir/$output_file'" 73 | python $script > $txt_output_dir/$output_file 74 | else 75 | echo "doing 'python $script'" 76 | python $script 77 | fi 78 | } 79 | 80 | # these scripts take longer to run and require source data. Run last. 81 | slow_scripts="crcns_hc-3.py crcns_ret-1.py crcns_ssc-1.py crcns_alm-1.py" 82 | all_scripts=`ls *.py` 83 | 84 | # first, run all scripts that do not take a long time 85 | for script in $all_scripts ; do 86 | if [[ $slow_scripts != *"$script"* ]] 87 | then 88 | run_script $script 89 | fi 90 | done 91 | 92 | 93 | # check if have source data (for scripts that take longer) 94 | 95 | if [[ "$have_source_data" == "0" ]] ; then 96 | echo $source_data_msg 97 | exit 0 98 | fi 99 | 100 | echo "" 101 | echo "Now running scripts that take longer..." 102 | 103 | for script in $slow_scripts ; do 104 | if [[ "$prompt_for_slow" == "y" ]] ; then 105 | yes_no "Run $script ?" 106 | if [[ "$yesno" == "y" ]] ; then 107 | run_script $script 108 | fi 109 | else 110 | run_script $script 111 | fi 112 | done 113 | 114 | echo "All done." 115 | 116 | 117 | exit 0 118 | -------------------------------------------------------------------------------- /examples/create_scripts/timeseries-e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | from nwb import nwb_file 4 | from nwb import nwb_utils as utils 5 | 6 | """ 7 | Example extending the format: using MyNewTimeSeries type. 8 | 9 | This example uses an extension specified in file "examples/e-timeseries.py". 10 | The extension specified in that file defines a new type of TimeSeries 11 | (named "MyNewTimeSeries", which illustrates how to create a new TimeSeries 12 | type. The code here uses the MyNewTimeSeries type to store data in 13 | /acquisition/timeseries 14 | 15 | 16 | The convention of having "e-" in front of the extension (and "-e" at the 17 | end of the create script name) is only used for these examples. Any name for the 18 | create script and extension(s) can be used as long as the actual name of the 19 | extension(s) are referenced by the create script and passed as parameters to 20 | nwb_validate.py when validating NWB files created using one or more extensions. 21 | 22 | 23 | """ 24 | # create a new NWB file 25 | OUTPUT_DIR = "../created_nwb_files/" 26 | file_name = __file__[0:-3] + ".nwb" 27 | 28 | settings = {} 29 | settings["file_name"] = OUTPUT_DIR + file_name 30 | settings["identifier"] = utils.create_identifier("MyNewTimeSeries example") 31 | settings["mode"] = "w" 32 | settings["start_time"] = "2016-04-07T03:16:03.604121" 33 | settings["description"] = "Test file demonstrating using a new TimeSeries type that was defined using an extension" 34 | 35 | # specify the extension (Could be more than one. Only one used now). 36 | settings['extensions'] = ["extensions/e-timeseries.py"] 37 | f = nwb_file.open(**settings) 38 | 39 | 40 | ######################################################################## 41 | # Make some sample data for the foo_timeseries 42 | 43 | data = [[1.2, 1.3, 1.4], [2.2, 2.3, 2.4], [3.2, 3.3, 3.4], [4.2, 4.3, 4.4], [5.2, 5.3, 5.4]] 44 | times = [0.1, 0.2, 0.3, 0.4, 0.5] 45 | 46 | # create an instance of MyNewTimeseries. Name of group will be "my_new_timeseries 47 | # it will be stored in /acquisition/timeseries 48 | 49 | nts = f.make_group("mnts:", "my_new_timeseries", path="/acquisition/timeseries", 50 | attrs={"source": "source of data for my new timeseries"} ) 51 | nts.set_dataset("data", data, attrs={"conversion": 1.0, "resolution": 0.001, "unit": "--unit goes here--"}) 52 | nts.set_dataset("timestamps", times) 53 | 54 | # specify metadata that is part of MyNewTimeSeries type 55 | nts.set_attr("foo", "This added to attribute 'foo'") 56 | nts.set_dataset("bar", [2, 4, 5, 6, 7]) 57 | 58 | # All done. Close the file 59 | f.close() 60 | 61 | -------------------------------------------------------------------------------- /examples/create_scripts/trajectorySeries-e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | import numpy as np 4 | from nwb import nwb_file 5 | from nwb import nwb_utils as utils 6 | 7 | """ 8 | Example of extending the format. 9 | 10 | This example uses an extension specified in file "examples/e-trajectorySeries.py". 11 | The extension specified in that file defines a new type of Timeseries 12 | (named "TrajectorySeries", which stores the the trajectory of a hand 13 | measured during a primate experiment with reaching behavior. 14 | 15 | The trajectories are stored from four sensors and each sensor has 16 | six degrees of freedom. 17 | 18 | TrajectorySeries is an extension of the SpatialSeries. The 19 | definition (i.e. extension) is in file extensions/e-trajectorySeries.py. 20 | 21 | This version uses datasets to specify the measurement names and values. 22 | (These could also be specified as text using the SpatialSeries reference_frame, 23 | dataset, but not in a defined, machine readable way). 24 | 25 | 26 | """ 27 | # create a new NWB file 28 | OUTPUT_DIR = "../created_nwb_files/" 29 | file_name = __file__[0:-3] + ".nwb" 30 | 31 | settings = {} 32 | settings["file_name"] = OUTPUT_DIR + file_name 33 | settings["identifier"] = utils.create_identifier("trajectorySeries example") 34 | settings["mode"] = "w" 35 | settings["start_time"] = "2016-04-07T03:16:03.604121" 36 | settings["description"] = "Test file demonstrating creating a new TimeSeries type using an extension" 37 | 38 | # specify the extension (Could be more than one. Only one used now). 39 | settings['extensions'] = ["extensions/e-trajectorySeries.py"] 40 | f = nwb_file.open(**settings) 41 | 42 | 43 | ######################################################################## 44 | # Make some sample data for the foo_timeseries 45 | 46 | data = np.linspace(1., 100.0, 6*4*1000).reshape(24,1000) 47 | times = np.linspace(0.0, 60.*2., 1000) 48 | 49 | # create an instance of MyNewTimeseries. Name of group will be "my_new_timeseries 50 | # it will be stored in /acquisition/timeseries 51 | 52 | nts = f.make_group("", "hand_position", path="/acquisition/timeseries", 53 | attrs={"source": "source of data for my new timeseries"} ) 54 | nts.set_dataset("data", data, attrs={"conversion": 1.0, "resolution": 0.001, "unit": "see measurements"}) 55 | nts.set_dataset("timestamps", times) 56 | 57 | # specify metadata that is part of MyNewTimeSeries type 58 | measurement_names = ["s1_x", "s1_y", "s1_z", "s1_r", "s1_t", "s1_o", 59 | "s2_x", "s2_y", "s2_z", "s2_r", "s2_t", "s2_o", 60 | "s3_x", "s3_y", "s3_z", "s3_r", "s3_t", "s3_o"] 61 | 62 | nts.set_attr("measurement_names", measurement_names) 63 | measurement_units = ["meter", "meter", "meter", "radian", "radian", "radian", 64 | "meter", "meter", "meter", "radian", "radian", "radian", 65 | "meter", "meter", "meter", "radian", "radian", "radian"] 66 | 67 | nts.set_attr("measurement_units", measurement_units) 68 | 69 | # All done. Close the file 70 | f.close() 71 | 72 | -------------------------------------------------------------------------------- /examples/create_scripts/trajectorySeries2-e.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | import numpy as np 4 | from nwb import nwb_file 5 | from nwb import nwb_utils as utils 6 | 7 | """ 8 | Example of extending the format. 9 | 10 | This example uses an extension specified in file "examples/e-trajectorySeries.py". 11 | The extension specified in that file defines a new type of Timeseries 12 | (named "TrajectorySeries", which stores the the trajectory of a hand 13 | measured during a primate experiment with reaching behavior. 14 | 15 | The trajectories are stored from four sensors and each sensor has 16 | six degrees of freedom. 17 | 18 | TrajectorySeries is an extension of the SpatialSeries. The 19 | definition (i.e. extension) is in file extensions/e-trajectorySeries2.py. 20 | 21 | This version specifies all the measurement units in advance in the extension. 22 | 23 | """ 24 | # create a new NWB file 25 | OUTPUT_DIR = "../created_nwb_files/" 26 | file_name = __file__[0:-3] + ".nwb" 27 | 28 | settings = {} 29 | settings["file_name"] = OUTPUT_DIR + file_name 30 | settings["identifier"] = utils.create_identifier("trajectorySeries example") 31 | settings["mode"] = "w" 32 | settings["start_time"] = "2016-04-07T03:16:03.604121" 33 | settings["description"] = "Test file demonstrating creating a new TimeSeries type using an extension" 34 | 35 | # specify the extension (Could be more than one. Only one used now). 36 | settings['extensions'] = ["extensions/e-trajectorySeries2.py"] 37 | f = nwb_file.open(**settings) 38 | 39 | 40 | ######################################################################## 41 | # Make some sample data 42 | 43 | data = np.linspace(1., 100.0, 6*4*1000).reshape(24,1000) 44 | times = np.linspace(0.0, 60.*2., 1000) 45 | 46 | # create an instance of MyNewTimeseries. Name of group will be "my_new_timeseries 47 | # it will be stored in /acquisition/timeseries 48 | 49 | nts = f.make_group("", "hand_position", path="/acquisition/timeseries", 50 | attrs={"source": "source of data for my new timeseries"} ) 51 | nts.set_dataset("data", data, attrs={"conversion": 1.0, "resolution": 0.001, 52 | "unit": "meter and radian; see definition of dimension trajectories in format specification"}) 53 | nts.set_dataset("timestamps", times) 54 | 55 | # specify meaning of variables 56 | reference_frame = ("Meaning of measurement values in array data, (e.g. sensor s1, s2, s3, s4; " 57 | "x, y, z, pitch, roll, yaw) should be described here") 58 | nts.set_dataset("reference_frame", reference_frame) 59 | 60 | # Add in sample epochs to specify the trials 61 | trial_times = [ [0.5, 1.5], [2.5, 3.0], [3.5, 4.0]] 62 | 63 | for trial_num in range(len(trial_times)): 64 | trial_name = "Trial_%03i" % (trial_num+1) 65 | start_time, stop_time = trial_times[trial_num] 66 | ep = utils.create_epoch(f, trial_name, start_time, stop_time) 67 | utils.add_epoch_ts(ep, start_time, stop_time, "hand_position", nts) 68 | 69 | 70 | # All done. Close the file 71 | f.close() 72 | 73 | -------------------------------------------------------------------------------- /examples/created_nwb_files/0_README.txt: -------------------------------------------------------------------------------- 1 | This directory, (examples/created_NWB_files) will contain NWB 2 | files that are created by running the scripts in 3 | directory ../create_scripts 4 | 5 | -------------------------------------------------------------------------------- /examples/text_output_files/0_README.txt: -------------------------------------------------------------------------------- 1 | Directory examples/text_output_files 2 | 3 | Contains text files generated by scripts. Subdirectories are: 4 | 5 | create - generated by create_scrips 6 | 7 | validate - generated by validate scripts (in ../utility_scripts directory) 8 | 9 | doc - generated documention files, created by scripts "make_docs.py" and "make_docs.sh" 10 | in ../utility_scripts directory. 11 | 12 | 13 | 14 | -------------------------------------------------------------------------------- /examples/text_output_files/create/0_README.txt: -------------------------------------------------------------------------------- 1 | Directory examples/text_output_files/create 2 | 3 | Will contain text file output of running script 4 | ../../create_scripts/run_all.sh 5 | 6 | 7 | -------------------------------------------------------------------------------- /examples/text_output_files/diff/0_README.txt: -------------------------------------------------------------------------------- 1 | Directory examples/text_output_files/diff 2 | 3 | Will contain output of running script ../../utility_scripts/h5diffci.sh 4 | and script ../../utility_scipts/make_cv_diff.sh 5 | 6 | -------------------------------------------------------------------------------- /examples/text_output_files/doc/0_README.txt: -------------------------------------------------------------------------------- 1 | Directory examples/text_output_files/doc 2 | 3 | Will contains documenation files created by script ../../utility_scripts/make_docs.sh 4 | 5 | -------------------------------------------------------------------------------- /examples/text_output_files/validate/0_README.txt: -------------------------------------------------------------------------------- 1 | Directory: examples/text_output_files/validate 2 | 3 | Will contains output of running ../../utility_scripts/validate_all.py 4 | 5 | -------------------------------------------------------------------------------- /examples/utility_scripts/0_README.txt: -------------------------------------------------------------------------------- 1 | Directory examples/utility_scripts 2 | 3 | Contains: 4 | 5 | h5diffci.sh - Demonstrates using h5diffci.py utility which displays difference between HDF5 files. 6 | 7 | make_cv_diff.sh - Makes diff of output of create and validate scripts. 8 | Useful to make sure they mostly match. If not there might be an error in software. 9 | 10 | make_docs.sh - Demonstrate making documentation. (Old version, does not generate docs 11 | for all extension examples). 12 | 13 | make_docs.py - Demonstrate making documentation. (New version). To run: python make_docs.py 14 | 15 | validate_all.py - Validates all NWB files created by create scripts. To run: python validate_all.py 16 | 17 | validate_internal.sh - Demo of validating file using internally stored format specifications. 18 | 19 | check_schemas.sh - Validate schema files (nwb_core.py and example extensions). 20 | 21 | cmp_created.sh - compare (diff) nwb files with the same names in two different directories, save 22 | output in third directory. 23 | 24 | install_source_data.py - download and install example/source_data_2 directory (which is needed 25 | to run some of the ../create_scripts 26 | 27 | make_h5sig.py - generate 'h5sig' (hdf5 signature) of nwb files that are in a directory, storing the 28 | generated signatures in an output directory. 29 | 30 | validate_others.sh - validates all nwb files in a directory, saving validation outout in an output 31 | directory. 32 | 33 | -------------------------------------------------------------------------------- /examples/utility_scripts/check_schemas.sh: -------------------------------------------------------------------------------- 1 | # Script to validate nwb_core specification and all example extensions. 2 | # Uses the nwb.check_schema utility (which in turn, uses the json-schema 3 | # specification in file meta_schema.py). 4 | 5 | # nwb.check_schema requires having jsonschema installed. 6 | # available at: https://github.com/Julian/jsonschema 7 | 8 | # to run, type ./check_schemas.sh 9 | 10 | # check core schema 11 | echo "doing: python -m nwb.check_schema N" 12 | python -m nwb.check_schema N 13 | 14 | # get list of extensions to check 15 | extensions=`ls ../create_scripts/extensions/e-*.py` 16 | 17 | # check schema for each extension 18 | for fn in $extensions 19 | do 20 | echo "doing: python -m nwb.check_schema $fn" 21 | python -m nwb.check_schema $fn 22 | done 23 | 24 | echo "All done" 25 | 26 | -------------------------------------------------------------------------------- /examples/utility_scripts/cmp_created.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # This script compares nwb files in two directories, saving the result 4 | # (showing differences) in a third directory. 5 | 6 | 7 | nwb1=$1 8 | nwb2=$2 9 | dest=$3 10 | if [ ! -d "$nwb1" ]; then 11 | nwb1="../created_nwb_files_py2" 12 | fi 13 | if [ ! -d "$nwb2" ]; then 14 | nwb2="../created_nwb_files_py3" 15 | fi 16 | if [ ! -d "$dest" ]; then 17 | dest="../text_output_files/diff/created_nwb23" 18 | fi 19 | if [ ! -d "$nwb1" ]; then 20 | echo "Directory nwb1, '$nwb1' does not exist" 21 | exit 1 22 | fi 23 | if [ ! -d "$nwb2" ]; then 24 | echo "Directory nwb2, '$nwb2' does not exist" 25 | exit 1 26 | fi 27 | if [ ! -d "$dest" ]; then 28 | echo "Directory dest, '$dest' does not exist" 29 | exit 1 30 | fi 31 | 32 | echo "comparing $nwb1/*.nwb to $nwb2/*.nwb, saving differences in $dest" 33 | # FILES=`find $nwb1 -name "*.nwb" -exec basename {} \;` 34 | FILES=`find -H $nwb1 -name "*.nwb"` 35 | for f in $FILES 36 | do 37 | bn=`basename $f` 38 | # Substring Removal 39 | path=${f#$nwb1} 40 | f_name=${bn%.*} 41 | file2="$nwb2$path" 42 | if [ ! -f "$file2" ]; then 43 | echo "Not found: $file2" 44 | continue 45 | fi 46 | echo "doing python -m nwb.h5diffsig $f $file2 > $dest/$f_name.txt" 47 | python -m nwb.h5diffsig $f $file2 > $dest/$f_name.txt 48 | done 49 | 50 | -------------------------------------------------------------------------------- /examples/utility_scripts/h5diffsig.sh: -------------------------------------------------------------------------------- 1 | 2 | echo "Demonstrate running HDF5 diff utility 'h5diffsig.py'" 3 | 4 | 5 | echo "This demo finds difference between:" 6 | echo " ../created_nwb_files/motion_correction.nwb, and:" 7 | echo " ../created_nwb_files/motion_correction2.nwb" 8 | echo 9 | echo "The difference is displaed on the screen, and saved" 10 | echo "in file: ../text_output_files/diff/motion_correction1_2_diff.txt" 11 | 12 | 13 | python -m nwb.h5diffsig ../created_nwb_files/motion_correction.nwb ../created_nwb_files/motion_correction2.nwb > \ 14 | ../text_output_files/diff/motion_correction1_2_diff.txt 15 | 16 | cat ../text_output_files/diff/motion_correction1_2_diff.txt 17 | 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /examples/utility_scripts/make_cv_diff.sh: -------------------------------------------------------------------------------- 1 | echo "This script creates a file showing the difference between" 2 | echo "the output of creating the NWB files and validating them." 3 | echo 4 | echo "It should only be run after runing scripts:" 5 | echo "../create_scripts/run_all.sh and validate_all.py" 6 | echo 7 | echo "Except for some warning messages, and any extra output" 8 | echo "generated by create scripts, the result of the diff should" 9 | echo "show that the output are mostly the same. If it is not," 10 | echo "the diffrence may indicate there is a bug in the software." 11 | 12 | diff -r ../text_output_files/create -x 0_README.txt ../text_output_files/validate > ../text_output_files/diff/cv_diff.txt 13 | 14 | echo 15 | echo "done creating diff." 16 | echo "It is stored in file '../text_output_files/diff/cv_diff.txt'" 17 | -------------------------------------------------------------------------------- /examples/utility_scripts/make_docs.py: -------------------------------------------------------------------------------- 1 | # This script demonstrates creating documentation for the NWB format." 2 | # 3 | # Documentation may be created for the core format alone, or the" 4 | # core format combined with one or more extensions." 5 | # 6 | # The documentation is generated from the format specifications." 7 | # The format specifications can be in standalone '.py' files or" 8 | # can be loaded from a created NWB file. The latter method " 9 | # is useful for generating documentaiton that is guaranteed to" 10 | # describe a particular NWB file." 11 | 12 | 13 | import sys 14 | import glob 15 | import os, fnmatch 16 | from subprocess import check_output 17 | from sys import version_info # py3 18 | 19 | # global constants 20 | txt_output_dir="../text_output_files/doc" 21 | nwb_dir="../created_nwb_files" 22 | 23 | 24 | # py3: convert bytes to str (unicode) if Python 3 25 | def make_str3(val): 26 | if isinstance(val, bytes) and version_info[0] > 2: 27 | return val.decode('utf-8') 28 | else: 29 | return val 30 | 31 | 32 | def do_command(cmd, output_file): 33 | """ execute command in cmd, write to output_file""" 34 | global txt_output_dir 35 | output_path = os.path.join(txt_output_dir, output_file) 36 | print ("doing: %s > %s" % (cmd, output_path)) 37 | output = check_output(cmd.split(" ")) 38 | with open(output_path, "w") as f: 39 | f.write(make_str3(output)) 40 | 41 | 42 | print ("documentation for core, e.g. file 'nwb_core.py'") 43 | cmd = "python -m nwb.make_docs" 44 | out = "core_doc.html" 45 | do_command(cmd, out) 46 | 47 | print ("documentation using two external extensions") 48 | cmd = ("python -m nwb.make_docs ../create_scripts/extensions/e-general.py," 49 | "../create_scripts/extensions/e-intracellular.py") 50 | out = "core_intra_gen.html" 51 | do_command(cmd, out) 52 | 53 | print ("documentation using schema's stored in created NWB files") 54 | nwb_files = glob.glob(os.path.join(nwb_dir, "*-e.nwb")) 55 | for file_path in nwb_files: 56 | base_name = os.path.basename(file_path)[0:-4] 57 | cmd = "python -m nwb.make_docs %s" % file_path 58 | out = "%s.html" % base_name 59 | do_command(cmd,out) 60 | 61 | sys.exit() 62 | 63 | -------------------------------------------------------------------------------- /examples/utility_scripts/make_docs.sh: -------------------------------------------------------------------------------- 1 | 2 | echo 3 | echo "This script demonstrates creating documentation for the NWB format." 4 | echo 5 | echo "Documentation may be created for the core format alone, or the" 6 | echo "core format combined with one or more extensions." 7 | echo 8 | echo "The documentation is generated from the format specifications." 9 | echo "The format specifications can be in standalone '.py' files or" 10 | echo "can be loaded from a created NWB file. The latter method " 11 | echo "is useful for generating documentaiton that is guaranteed to" 12 | echo "describe a particular NWB file." 13 | 14 | echo 15 | echo "Making core doc by doing:" 16 | cmd="python -m nwb.make_docs > ../text_output_files/doc/core_doc.html" 17 | echo "$cmd" 18 | python -m nwb.make_docs > ../text_output_files/doc/core_doc.html 19 | 20 | echo 21 | echo "Making core doc with two extensions by doing:" 22 | cmd="python -m nwb.make_docs ../create_scripts/extensions/e-intracellular.py,../create_scripts/extensions/e-general.py > \ 23 | ../text_output_files/doc/core_intra_gen.html" 24 | echo "$cmd" 25 | python -m nwb.make_docs ../create_scripts/extensions/e-intracellular.py,../create_scripts/extensions/e-general.py > \ 26 | ../text_output_files/doc/core_intra_gen.html 27 | 28 | echo 29 | echo "Making documentation from created NWB file by doing:" 30 | cmd="python -m nwb.make_docs ../created_nwb_fles/interface-e.nwb > ../text_output/doc/interface-e.html" 31 | echo "$cmd" 32 | python -m nwb.make_docs ../created_nwb_files/interface-e.nwb > ../text_output_files/doc/interface-e.html 33 | 34 | -------------------------------------------------------------------------------- /examples/utility_scripts/make_pdf_doc.sh: -------------------------------------------------------------------------------- 1 | # this script generates PDF files from html files, adding page numbers 2 | # it requires the "wkhtmltopdf" utility be installed 3 | 4 | if [ "$#" -ne 2 ]; then 5 | script_name=${0##*/} 6 | echo "Requires two command-line arguments:" 7 | echo " " 8 | echo "Example:" 9 | echo "./$script_name ../text_output_files/doc/ nwb_file_format_specification_1.0.3_beta" 10 | exit 1 11 | fi 12 | 13 | docdir=$1 14 | base_name=$2 15 | html="$base_name.html" 16 | pdf="$base_name.pdf" 17 | 18 | echo "doc dir=$docdir" 19 | echo "html file=$html" 20 | echo "pdf file=$pdf" 21 | 22 | wd=`pwd` 23 | cd $docdir 24 | wkhtmltopdf --footer-center [page]/[topage] $html $pdf 25 | cd $wd 26 | 27 | 28 | -------------------------------------------------------------------------------- /examples/utility_scripts/validate_behavior.py: -------------------------------------------------------------------------------- 1 | # script demonstrating use of validate_file routine called from Python. 2 | 3 | from nwb import nwb_validate as nwbv 4 | 5 | file = "../created_nwb_files/behavior.nwb" 6 | validation_result = nwbv.validate_file(file, verbosity="none") 7 | 8 | print "validated", file 9 | print "validation_result=", validation_result 10 | print "all done" 11 | 12 | -------------------------------------------------------------------------------- /examples/utility_scripts/validate_internal.sh: -------------------------------------------------------------------------------- 1 | edho 2 | echo "This script demonstrates validating an NWB file using the format" 3 | echo "specifications stored within the file." 4 | 5 | if [[ ! -e "../created_nwb_files/annotations.nwb" ]] ; then 6 | echo "This script requires file ../created_nwb_files/annotations.nwb" 7 | echo "do: python ../create_scripts/annotations.py to create that file" 8 | echo "before runnign this script" 9 | exit 1 10 | fi 11 | 12 | # Note the two dashes after the file name. First dash is for 13 | # extensions, second is for the core specification (nwb_core.py). 14 | 15 | python -m nwb.nwb_validate ../created_nwb_files/annotations.nwb - - 16 | 17 | 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /examples/utility_scripts/validate_others.sh: -------------------------------------------------------------------------------- 1 | # script to validate all NWB files stored in a directory, sending 2 | # output to another directory. 3 | # Validation is done using the external "nwb_core.py" definition and 4 | # not using any schema's included in the file. So it will not if 5 | # the nwb files were created using extensions. To validate files 6 | # that use extensions, eiter the extensions need to be specified in 7 | # the command line or using the specifications stored in the file 8 | # need to be specified. Examples of validations using these methods 9 | # are respectively in the scripts "validate_all.py" and 10 | # "validate_internal.sh" 11 | 12 | if [[ ! "$#" -eq 2 ]] ; then 13 | echo "Format is:" 14 | echo "$0 " 15 | echo "where:" 16 | echo " - directory containing nwb files" 17 | echo " - directory for validation output" 18 | exit 1 19 | fi 20 | 21 | nwb_dir=$1 22 | out_dir=$2 23 | 24 | if [[ ! -d "$nwb_dir" ]] ; then 25 | echo " does not exist: $nwb_dir" 26 | exit 1 27 | fi 28 | 29 | 30 | if [[ ! -d "$out_dir" ]] ; then 31 | echo " does not exist: $out_dir" 32 | exit 1 33 | fi 34 | 35 | # get list of nwb files 36 | files=`ls $nwb_dir/*.nwb` 37 | 38 | if [[ "$files" == "" ]] ; then 39 | echo "No files with extension '.nwb' found in : $nwb_dir" 40 | exit 1 41 | fi 42 | 43 | # validate each file 44 | for nwb_file in $files 45 | do 46 | fname_and_extension=${nwb_file##*/} 47 | fn=${fname_and_extension%.nwb} 48 | # fn="${nwb_file%.*}" 49 | echo "doing: python -m nwb.validate $nwb_dir/$fn.nwb > $out_dir/$fn.txt" 50 | python -m nwb.validate $nwb_dir/$fn.nwb > $out_dir/$fn.txt 51 | # if [ $? -ne 0 ]; then 52 | # echo "python -m nwb.validate $nwb_dir/$fn.nwb FAILED" 53 | # exit 1 54 | # fi 55 | done 56 | 57 | # echo "All done" 58 | 59 | -------------------------------------------------------------------------------- /matlab_bridge/0_README.txt: -------------------------------------------------------------------------------- 1 | 0_README.txt for NWB matlab_bridge API 2 | 3 | The matlab_bridge implements a matlab API to the NWB format by interfacing 4 | matlab to the Python NWB API. 5 | 6 | See file 0_INSTALL.txt for instructions about how to install the matlab_bridge 7 | API. 8 | 9 | Directories are: 10 | 11 | matlab_examples - matlab scripts used to create sample NWB files 12 | 13 | matlab_unittest - matlab unittests 14 | 15 | matlab_bridge_api - software implementing the matlab bridge API 16 | 17 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_bridge_api/+h5g8/dataset.m: -------------------------------------------------------------------------------- 1 | classdef dataset < h5g8.node 2 | %Class for nwb dataset objects 3 | methods 4 | function obj = dataset(ml_f, fg_dataset) 5 | % create a matlab nwb_dataset that wraps the Python fg_dataset 6 | obj = obj@h5g8.node(ml_f, fg_dataset); 7 | end 8 | end 9 | end 10 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_bridge_api/+h5g8/node.m: -------------------------------------------------------------------------------- 1 | classdef node < handle 2 | % This class (node) is group or dataset object in matlab 3 | % Corresponds to Node in h5gate (Python) 4 | 5 | properties 6 | ml_file % matlat file object 7 | fg_node % file gate (Python, h5gate) node object 8 | end 9 | 10 | methods 11 | function obj = node(ml_file, fg_node) 12 | % save reference matlab file and h5gate (python) node 13 | obj.ml_file = ml_file; 14 | obj.fg_node = fg_node; 15 | end 16 | function [robj] = set_attr(obj, aid, value, varargin) 17 | % Set attribute with key aid to value 'value' 18 | % if custom true, don't give warning about custom attribute 19 | % parameters for h5gate set_attr: 20 | % (self, aid, value, custom=''): 21 | arg_names = { 'custom'}; 22 | arg_types = { 'logical' }; 23 | arg_default={ false }; 24 | arg_vals = obj.ml_file.parse_arguments(varargin, arg_names, arg_types, arg_default); 25 | custom = arg_vals.custom; 26 | % flatten attribute value if necessary 27 | [val1d, shape] = obj.ml_file.flatten(value); 28 | % attrs = {aid, value}; 29 | % [atrs1d, attrs_shape] = obj.ml_file.flatten_attrs(attrs); % modifies attrs 30 | % fvalue = atrs1d(2); % flattened value 31 | % call python code in h5g8 32 | % obj.fg_node.set_attr(aid, value, custom); 33 | obj.fg_node.set_attr(aid, val1d, custom, shape); 34 | % this call the matlab group constructor 35 | % obj.ml_file.process_h5commands() 36 | % return original node object to allow stacking calls to this 37 | robj = obj; 38 | end 39 | end 40 | 41 | end 42 | 43 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_bridge_api/nwb_file.m: -------------------------------------------------------------------------------- 1 | function [f] = nwb_file(varargin) 2 | % parameters to Python nwb_file.open are: 3 | % start_time=None, mode="w-", identifier=None, description=None, core_spec="nwb_core.py", extensions=[], default_ns="core", keep_original=False, auto_compress=True) 4 | arg_names = { 'file_name', 'start_time', 'mode', 'identifier', 'description', 'core_spec', 'extensions', 'default_ns', 'keep_original', 'auto_compress', 'verbosity' }; 5 | arg_types = { 'char', 'char', 'char', 'char', 'char', 'char', 'cell', 'char', 'logical', 'logical', 'char'}; 6 | arg_default={ '', '', 'w-', '', '', 'nwb_core.py', {}, 'core', false, true, 'all' }; 7 | arg_vals = parse_arguments(varargin, arg_names, arg_types, arg_default); 8 | % check for correct parameter values 9 | file_name = arg_vals.file_name; 10 | if isempty(file_name) 11 | error('Must specify file name, e.g. "test.nwb"') 12 | end 13 | % fprintf('in nwb_file, file_name=%s', file_name) 14 | mode = arg_vals.mode; 15 | valid_modes = {'r', 'r+', 'w', 'w-', 'a'}; 16 | if ~isa(mode, 'char') || ~(nnz(strcmp(mode, valid_modes)) == 1) 17 | error('Invalid mode (%s). Must be one of: %s', mode, strjoin(valid_modes,', ')) 18 | end 19 | file_exists = (exist(file_name, 'file') == 2); 20 | if ~file_exists && (nnz(strcmp(mode, {'r', 'r+'})) == 1) 21 | error('File not found (%s). File must exist to use mode "r" or "r+"', file_name) 22 | end 23 | creating_file = (strcmp(mode, 'w') || (nnz(strcmp(mode, {'a', 'w-'}))==1 && ~file_exists)); 24 | identifier = arg_vals.identifier; 25 | description = arg_vals.description; 26 | if creating_file 27 | % creating a new file. identifier and description required. 28 | if ~isa(identifier, 'char') || strcmp(identifier, '') 29 | error('When creating a file, "identifier" must be specified and be a string') 30 | end 31 | if ~isa(identifier, 'char') || strcmp(description, '') 32 | error('When creating a file, "description" must be specified and be a string') 33 | end 34 | end 35 | extensions = arg_vals.extensions; 36 | if ~iscellstr(extensions) 37 | error('extensions must be a cell array of strings') 38 | end 39 | % setup options for h5gate 40 | % previously had: 'custom_node_identifier', {'schema_id', 'Custom'}, ... 41 | options = {'mode', mode, ... 42 | 'keep_original', arg_vals.keep_original, ... 43 | 'auto_compress', arg_vals.auto_compress, ... 44 | 'custom_node_identifier', {'neurodata_type', 'Custom'}, ... 45 | 'verbosity', arg_vals.verbosity}; 46 | if strcmp(arg_vals.core_spec, '-') 47 | spec_files = extensions; 48 | else 49 | spec_files = {extensions{:}, arg_vals.core_spec}; 50 | end 51 | % open file 52 | f = h5g8.file(file_name, spec_files, arg_vals.default_ns, options); 53 | % set initial metadata 54 | py.nwb.nwb_init.nwb_init(f.fg_file, mode, arg_vals.start_time, identifier, description, creating_file) 55 | end 56 | 57 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_bridge_api/parse_arguments.m: -------------------------------------------------------------------------------- 1 | function [arg_vals] = parse_arguments(args, arg_names, arg_types, arg_default) 2 | % parse variable arguements passed to function, return 3 | % values for each defined in arg_defs. arg_names has argument 4 | % names, arg_types, the expected type, either 'char' (string) or 'cell' 5 | % 'cell' is cell array used for list of alternate key, values 6 | % set up default values to empty string or empty cell array 7 | arg_vals = struct; 8 | for i=1:numel(arg_names) 9 | arg_vals.(arg_names{i}) = arg_default{i}; 10 | end 11 | found_named_arg = ''; 12 | i = 1; 13 | while i <= numel(args) 14 | arg = args{i}; 15 | if ischar(arg) && ismember(arg, arg_names) 16 | % found named argument 17 | val = args{i+1}; 18 | [~, idx] = ismember(arg, arg_names); 19 | if ~strcmp(class(val), arg_types{idx}) 20 | error('Unexpected type (%s) for parameter "%s", expecting "%s"', ... 21 | class(val), arg, arg_types{i}) 22 | end 23 | found_named_arg = arg; 24 | arg_vals.(arg) = val; 25 | i = i + 2; 26 | continue 27 | end 28 | if found_named_arg 29 | error('Unnamed argument appears after named argument "%s"', ... 30 | found_named_arg) 31 | end 32 | % maybe found valid un-named argument 33 | if i > numel(arg_names) 34 | error('Too many un-named arguments in function call'); 35 | end 36 | if ~strcmp(class(arg), arg_types{i}) 37 | error('Unnamed argment "%s" is type "%s"; expected type "%s"', ... 38 | arg_names{i}, class(arg), arg_types{i}); 39 | end 40 | % seems to be valid, save it 41 | arg_vals.(arg_names{i}) = arg; 42 | i = i + 1; 43 | end 44 | end 45 | 46 | 47 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_bridge_api/test_nwb.m: -------------------------------------------------------------------------------- 1 | function [ result ] = test_nwb( ) 2 | % - tests calling h5gate matlab interface 3 | OUTPUT_DIR = './'; % '../created_nwb_files/'; 4 | file_name = 'test_ml.nwb'; 5 | settings = { ... 6 | 'file_name', [OUTPUT_DIR file_name], ... 7 | 'identifier', char(py.nwb.nwb_utils.create_identifier('matlab test')), ... 8 | 'mode', 'w', ... 9 | 'start_time', '2016-04-07T03:16:03.604121', ... 10 | 'description','Test file created using matlab bridge'}; 11 | f = nwb_file(settings{:}); 12 | % f.set_dataset('experimenter', 'Jeff Teeters'); 13 | f.set_dataset('experimenter', 'Jeff Teeters'); 14 | g = f.make_group('', 'shank_01','attrs', {'happy', 'day'}); 15 | g.set_dataset('description', 'Test shank, with four recording sites'); 16 | m = f.make_group('', 'shank_01', 'attrs', {'Its', 'working'} ); 17 | lfp = m.make_group('LFP'); 18 | ts = lfp.make_group('', 'LFP_Timeseries'); 19 | ts.set_attr('source', 'moms backyard'); 20 | ts.set_attr('source2', 'moms new backyard with bunnies'); 21 | data = [ 1.2 1.3 1.4; 1.5 1.6 1.7 ]; 22 | % data = zeros(10000, 1); 23 | times = [ 0.12, 0.13, 0.14, 0.15, 0.16 ]; 24 | d = ts.set_dataset('data', data, 'compress', true); 25 | d.set_attr('unit', 'light_years'); 26 | ts.set_dataset('timestamps', times); 27 | ts.set_dataset('num_samples', int64(5)); 28 | % make some custom datasets 29 | g = f.make_custom_group('custom_subject_info', 'path', '/', 'attrs', {'upc', 'polly45'}); 30 | g.set_custom_dataset('dog_breed', 'Saint Bernard'); 31 | g.make_custom_group('lab_cats', 'attrs', {'info', 'this for help with cats', 'more_info', 'many more cats'}); 32 | f.set_custom_dataset('custom_dataset', 'blue_sky', 'path', '/cust_info', 'attrs', {'info', 'about the blue sky'}); 33 | g2 = f.get_node('/general/experimenter'); 34 | fprintf('found ml_node, path is %s\n',char(g2.fg_node.full_path)); 35 | f.close(); 36 | fprintf('done'); 37 | result = 0; 38 | end 39 | 40 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_examples/0_README.txt: -------------------------------------------------------------------------------- 1 | 0_README.txt for NWB MatLab examples 2 | 3 | Directories are: 4 | 5 | create_scripts - scripts used to create sample NWB files 6 | 7 | created_nwb_files - location of where example NWB files will be created 8 | 9 | text_output_files - location for storing output of unittests and examples 10 | This directory is created by scripts that run the 11 | unittests and examples. 12 | 13 | ../../examples/source_data_2 (Not located here, but needs to be installed 14 | in order to run the crcns_alm_1.m example script). This directory is 15 | installed by the "install_source_data.py" script in directory 16 | ../../examples/utility_scripts. 17 | 18 | To run the create_scripts, go into the directory (in Matlab) and run 19 | the script by typing the name into the command line. 20 | 21 | *** These require that the matlab NWB bridge is setup. See the instructions 22 | in the 0_INSTALL.txt file in the directory above this one. 23 | 24 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_examples/create_scripts/0_README.txt: -------------------------------------------------------------------------------- 1 | This directory "matlab_bridge/matlab_examples/create_scripts" contains example 2 | matlab scripts to create example NWB files. 3 | 4 | To run these scripts first install the matlab bridge as described in 5 | file mablab_bridge/0_INSTALL.txt 6 | 7 | Then to run the scripts, cd to this directory in matlab. Type 8 | the name of each script to run it, or "run_all_scripts" to 9 | run them all. 10 | 11 | Several types of scripts require additional files. These are: 12 | 13 | 14 | (1) Scripts that required input data. 15 | 16 | Scripts with with name starting with "crcns") require data in the 17 | "../source_data" directory. This data must be downloaded 18 | and placed inside the ../source_data directory. Instructions 19 | for doing this are in the examples/0_README.txt file 20 | (i.e. the readme in the directory above this one). 21 | 22 | 23 | (2) Scripts that require extensions. 24 | 25 | Scripts that have name ending with "-e.py" require one or more "extensions" 26 | (files that define extensions to the NWB format). The extensions are 27 | stored in directory "extensions". Usually the name of the extension 28 | used with the script will be the same as the name of the create script, 29 | except "e-" will be in front of the extension. 30 | 31 | The convention of having "e-" in front of the extension (and "-e" at the 32 | end of the create script name) is only used for these examples. Any name for the 33 | create script and extension(s) can be used as long as the actual name of the 34 | extension(s) are referenced by the create script and passed as parameters to 35 | nwb_validate.py when validating NWB files created using one or more extensions. 36 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_examples/create_scripts/analysis_e.m: -------------------------------------------------------------------------------- 1 | function analysis_e() 2 | 3 | % This example illustrates using an extension to store data in the the /analysis group. 4 | % The /analysis group is reserved for results of lab-specific analysis. 5 | % 6 | % The extension definition is in file "extensions/e-analysis.py". 7 | % 8 | % The example is based on the contents of the Allen Institute for Brain Science 9 | % Cell Types database NWB files. 10 | 11 | 12 | OUTPUT_DIR = '../created_nwb_files/'; 13 | script_base_name = mfilename(); 14 | nwb_file_name = [script_base_name '.nwb']; 15 | nwb_file_path = [OUTPUT_DIR nwb_file_name]; 16 | 17 | % create a new NWB file 18 | settings = { ... 19 | 'file_name', nwb_file_path, ... 20 | 'identifier', ... 21 | char(py.nwb.nwb_utils.create_identifier('abstract-feature example')), ... 22 | 'mode', 'w', ... 23 | 'start_time', 'Sat Jul 04 2015 3:14:16', ... 24 | 'description',['Test file demonstrating storing data in the /analysis' ... 25 | ' group that is defined by an extension.'] ... 26 | 'extensions', {'../../../examples/create_scripts/extensions/e-analysis.py'} ... 27 | }; 28 | 29 | fprintf('Creating %s', nwb_file_path); 30 | f = nwb_file(settings{:}); 31 | 32 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 33 | % This example, stores spike times for multiple sweeps 34 | % create the group for the spike times 35 | % The group ("aibs_spike_times") is defined in the extension 36 | 37 | ast = f.make_group('aibs_spike_times'); 38 | 39 | % some sample data 40 | times = [1.1, 1.2, 1.3, 1.4, 1.5]; 41 | 42 | % create some sample sweeps 43 | for i = 1:5 44 | sweep_name = sprintf('sweep_%03i', i); 45 | ast.set_dataset('', times, 'name', sweep_name); 46 | end 47 | 48 | % all done; close the file 49 | f.close() 50 | 51 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_examples/create_scripts/run_all_examples.m: -------------------------------------------------------------------------------- 1 | function run_all_examples() 2 | % runs all examples. Created nwb files are stored 3 | % in directory ../created_nwb_files 4 | 5 | % if nargin < 1 6 | % % default 'none' to display no validation information (other than if the test 7 | % % passes). Other options are: 'all', 'summary' 8 | % verbosity = 'none'; 9 | % end 10 | 11 | % directory for text output 12 | create_dir = '../text_output_files/create'; 13 | if ~exist(create_dir, 'dir') 14 | mkdir(create_dir); 15 | end 16 | 17 | % find all examples 18 | mfiles = dir('*.m'); 19 | script_name = mfilename(); 20 | % run each example 21 | for i = 1:length(mfiles) 22 | mfile = mfiles(i).name; 23 | [trash, name] = fileparts(mfile); % strip off .m extension 24 | if ~strcmp(name, script_name) 25 | % not this script, so run it 26 | log_file = [create_dir '/' name '.txt' ]; 27 | cmd = [ name, '();' ]; 28 | fprintf('\n========= Running %s\n', cmd) 29 | [T] = evalc(cmd); 30 | % save output 31 | fileID = fopen(log_file,'w'); 32 | fprintf(fileID, T); 33 | fclose(fileID); 34 | % diary(log_file) 35 | % run(cmd) 36 | % diary off 37 | end 38 | end 39 | 40 | % fprintf('\n========= Running abstract_feature()\n') 41 | % abstract_feature() 42 | % fprintf('\n========= Running analysis-e()\n') 43 | % analysis-e() 44 | % fprintf('\n========= Running crcns_alm_1()\n') 45 | % crcns_alm_1() 46 | 47 | end 48 | 49 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_examples/created_nwb_files/0_README.txt: -------------------------------------------------------------------------------- 1 | This directory, (matlab_bridge/matlab_examples/created_NWB_files) will 2 | contain NWB files that are created by running the scripts in 3 | directory ../create_scripts 4 | 5 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/run_all_tests.m: -------------------------------------------------------------------------------- 1 | function run_all_tests( verbosity ) 2 | %Run all the tests, Set input verbosity == 'all' to display 3 | % validation output for each NWB file created 4 | 5 | if nargin < 1 6 | % default 'none' to display no validation information (other than if the test 7 | % passes). Other options are: 'all', 'summary' 8 | verbosity = 'none'; 9 | end 10 | 11 | fprintf('pyversion is;') 12 | pyversion 13 | 14 | % directory for text output 15 | output_dir = '../matlab_examples/text_output_files'; 16 | if ~exist(output_dir, 'dir') 17 | mkdir(output_dir); 18 | end 19 | 20 | % write log of running all tests to the following file 21 | log_file='../matlab_examples/text_output_files/unittest_results.txt'; 22 | % delete '../matlab_examples/text_output_files/unittest_results.txt' 23 | if exist(log_file, 'file')==2 24 | delete(log_file); 25 | end 26 | diary(log_file) 27 | 28 | % find all test 29 | tests = dir('t_*.m'); 30 | script_name = mfilename(); 31 | % run each test 32 | for i = 1:length(tests) 33 | test = tests(i).name; 34 | [trash, name] = fileparts(test); % strip off .m extension 35 | if ~strcmp(name, script_name) 36 | % file is not this script, run it 37 | feval(name, verbosity); 38 | end 39 | end 40 | diary off 41 | end 42 | 43 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_annotation.m: -------------------------------------------------------------------------------- 1 | function t_annotation(verbosity) 2 | 3 | % test creation of annotation time series 4 | % TESTS AnnotationSeries creation 5 | % TESTS TimeSeries ancestry 6 | 7 | script_base_name = mfilename(); 8 | script_name = [script_base_name '.m']; 9 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 10 | if nargin < 1 11 | % default, display all information. Other options are: 'none', 'summary' 12 | verbosity = 'all'; 13 | end 14 | 15 | 16 | function test_annotation_series() 17 | name = 'annot'; 18 | % create_annotation_series(fname, name, 'acquisition') 19 | create_annotation_series(fname, name, 'acquisition/timeseries'); 20 | test_utils.verify_timeseries(fname, name, 'acquisition/timeseries', 'TimeSeries'); 21 | test_utils.verify_timeseries(fname, name, 'acquisition/timeseries', 'AnnotationSeries'); 22 | % create_annotation_series(fname, name, 'stimulus'); 23 | create_annotation_series(fname, name, 'stimulus/presentation'); 24 | test_utils.verify_timeseries(fname, name, 'stimulus/presentation', 'TimeSeries'); 25 | test_utils.verify_timeseries(fname, name, 'stimulus/presentation', 'AnnotationSeries'); 26 | end 27 | 28 | function create_annotation_series(fname, name, target) 29 | settings = { ... 30 | 'file_name', fname, 'verbosity', verbosity, ... 31 | 'identifier', nwb_utils.create_identifier('annotation example'), ... 32 | 'mode', 'w', ... 33 | 'start_time', 'Sat Jul 04 2015 3:14:16', ... 34 | 'description','Test file with AnnotationSeries' ... 35 | }; 36 | f = nwb_file(settings{:}); 37 | % annot = neurodata.create_timeseries('AnnotationSeries', name, target) 38 | annot = f.make_group('', name, 'path', ['/', target]); 39 | 40 | % annot.set_description('This is an AnnotationSeries with sample data') 41 | annot.set_attr('description', 'This is an AnnotationSeries with sample data'); 42 | % annot.set_comment('The comment and description fields can store arbitrary human-readable data') 43 | annot.set_attr('comments', 'The comment and desscription fields can store arbitrary human-readable data'); 44 | % annot.set_source('Observation of Dr. J Doe') 45 | annot.set_attr('source', 'Observation of Dr. J Doe'); 46 | % 47 | % annot.add_annotation('Rat in bed, beginning sleep 1', 15.0) 48 | % annot.add_annotation('Rat placed in enclosure, start run 1', 933.0) 49 | % annot.add_annotation('Rat taken out of enclosure, end run 1', 1456.0) 50 | % annot.add_annotation('Rat in bed, start sleep 2', 1461.0) 51 | % annot.add_annotation('Rat placed in enclosure, start run 2', 2401.0) 52 | % annot.add_annotation('Rat taken out of enclosure, end run 2', 3210.0) 53 | % annot.add_annotation('Rat in bed, start sleep 3', 3218.0) 54 | % annot.add_annotation('End sleep 3', 4193.0) 55 | % store pretend data 56 | % all time is stored as seconds 57 | andata = {}; 58 | andata{end+1} = {'Rat in bed, beginning sleep 1', 15.0}; 59 | andata{end+1} = {'Rat placed in enclosure, start run 1', 933.0}; 60 | andata{end+1} = {'Rat taken out of enclosure, end run 1', 1456.0}; 61 | andata{end+1} = {'Rat in bed, start sleep 2', 1461.0}; 62 | andata{end+1} = {'Rat placed in enclosure, start run 2', 2401.0}; 63 | andata{end+1} = {'Rat taken out of enclosure, end run 2', 3210.0}; 64 | andata{end+1} = {'Rat in bed, start sleep 3', 3218.0}; 65 | andata{end+1} = {'End sleep 3', 4193.0}; 66 | shape = [1, length(andata)]; 67 | annotations = cell(shape); 68 | times = zeros(shape); 69 | for i = 1:length(andata) 70 | annotations{i} = andata{i}{1}; 71 | times(i) = andata{i}{2}; 72 | end 73 | annot.set_dataset('data',annotations); 74 | annot.set_dataset('timestamps', times); 75 | f.close() 76 | end 77 | 78 | test_annotation_series() 79 | fprintf('%s PASSED\n', script_name); 80 | end 81 | 82 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_append.m: -------------------------------------------------------------------------------- 1 | function t_append(verbosity) 2 | 3 | % test opening file in append mode 4 | % TESTS modifying existing file 5 | % TESTS creation of modification_time 6 | % TESTS addition of TimeSeries to existing file 7 | % TESTS preservation of TimeSeries when file modified 8 | 9 | script_base_name = mfilename(); 10 | script_name = [script_base_name '.m']; 11 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 12 | if nargin < 1 13 | % default, display all information. Other options are: 'none', 'summary' 14 | verbosity = 'all'; 15 | end 16 | 17 | function test_append() 18 | name1 = 'annot1'; 19 | name2 = 'annot2'; 20 | % create_annotation_series(fname, name1, 'acquisition', True) 21 | create_annotation_series(fname, name1, 'acquisition/timeseries', true); 22 | % create_annotation_series(fname, name2, 'acquisition', False) 23 | create_annotation_series(fname, name2, 'acquisition/timeseries', false); 24 | test_utils.verify_timeseries(fname, name1, 'acquisition/timeseries', 'TimeSeries'); 25 | test_utils.verify_timeseries(fname, name1, 'acquisition/timeseries', 'AnnotationSeries'); 26 | test_utils.verify_timeseries(fname, name2, 'acquisition/timeseries', 'TimeSeries'); 27 | test_utils.verify_timeseries(fname, name2, 'acquisition/timeseries', 'AnnotationSeries'); 28 | % ut.verify_attribute_present(fname, 'file_create_date', 'modification_time') 29 | end 30 | 31 | 32 | function create_annotation_series(fname, name, target, newfile) 33 | if newfile 34 | settings = {'file_name', fname, 'verbosity', verbosity, ... 35 | 'identifier', ... 36 | char(py.nwb.nwb_utils.create_identifier('append example')), ... 37 | 'mode', 'w', ... 38 | 'start_time', 'Sat Jul 04 2015 3:14:16', ... 39 | 'description','Test append file'}; 40 | else 41 | settings = {'file_name', fname, 'mode', 'r+', 'verbosity', verbosity}; 42 | end 43 | f = nwb_file(settings{:}); 44 | % 45 | % annot = neurodata.create_timeseries('AnnotationSeries', name, target) 46 | annot = f.make_group('', name, 'path', ['/', target]); 47 | % annot.set_description('This is an AnnotationSeries '%s' with sample data' % name) 48 | % annot.set_comment('The comment and description fields can store arbitrary human-readable data') 49 | % annot.set_source('Observation of Dr. J Doe') 50 | annot.set_attr('description', sprintf('This is an AnnotationSeries ''%s'' with sample data', name)); 51 | annot.set_attr('comments', 'The comment and description fields can store arbitrary human-readable data'); 52 | annot.set_attr('source', 'Observation of Dr. J Doe'); 53 | 54 | % 55 | % annot.add_annotation('Rat in bed, beginning sleep 1', 15.0) 56 | % annot.add_annotation('Rat placed in enclosure, start run 1', 933.0) 57 | % annot.add_annotation('Rat taken out of enclosure, end run 1', 1456.0) 58 | % annot.add_annotation('Rat in bed, start sleep 2', 1461.0) 59 | % annot.add_annotation('Rat placed in enclosure, start run 2', 2401.0) 60 | % annot.add_annotation('Rat taken out of enclosure, end run 2', 3210.0) 61 | % annot.add_annotation('Rat in bed, start sleep 3', 3218.0) 62 | % annot.add_annotation('End sleep 3', 4193.0) 63 | % 64 | andata = {}; 65 | andata{end+1} = {'Rat in bed, beginning sleep 1', 15.0}; 66 | andata{end+1} = {'Rat placed in enclosure, start run 1', 933.0}; 67 | andata{end+1} = {'Rat taken out of enclosure, end run 1', 1456.0}; 68 | andata{end+1} = {'Rat in bed, start sleep 2', 1461.0}; 69 | andata{end+1} = {'Rat placed in enclosure, start run 2', 2401.0}; 70 | andata{end+1} = {'Rat taken out of enclosure, end run 2', 3210.0}; 71 | andata{end+1} = {'Rat in bed, start sleep 3', 3218.0}; 72 | andata{end+1} = {'End sleep 3', 4193.0}; 73 | shape = [1, length(andata)]; 74 | annotations = cell(shape); 75 | times = zeros(shape); 76 | for i = 1:length(andata) 77 | annotations{i} = andata{i}{1}; 78 | times(i) = andata{i}{2}; 79 | end 80 | annot.set_dataset('data',annotations); 81 | annot.set_dataset('timestamps', times); 82 | f.close() 83 | end 84 | 85 | test_append() 86 | fprintf('%s PASSED\n', script_name); 87 | end 88 | 89 | 90 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_epoch_tag.m: -------------------------------------------------------------------------------- 1 | function t_epoch_tag(verbosity) 2 | 3 | % create two epochs, add different subset of tags to each 4 | % verify main epoch folder has tag attribute that contains 5 | % exactly the unique tags of each epoch and that each 6 | % epoch contains the assigned tags 7 | 8 | script_base_name = mfilename(); 9 | script_name = [script_base_name '.m']; 10 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 11 | if nargin < 1 12 | % default, display all information. Other options are: 'none', 'summary' 13 | verbosity = 'all'; 14 | end 15 | 16 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 17 | 'identifier', nwb_utils.create_identifier('Epoch tags'), ... 18 | 'description','softlink test'}; 19 | f = nwb_file(settings{:}); 20 | 21 | tags = {'tag-a', 'tag-b', 'tag-c'}; 22 | 23 | % epoch1 = borg.create_epoch('epoch-1', 0, 3); 24 | 25 | epoch1 = f.make_group('', 'epoch-1'); 26 | epoch1.set_dataset('start_time', 0); 27 | epoch1.set_dataset('stop_time', 3); 28 | 29 | % for i in range(len(tags)-1): 30 | % epoch1.add_tag(tags[i+1]) 31 | epoch1.set_dataset('tags', tags(2:end)); 32 | 33 | % epoch2 = borg.create_epoch('epoch-2', 1, 4); 34 | epoch2 = f.make_group('', 'epoch-2'); 35 | epoch2.set_dataset('start_time', 1); 36 | epoch2.set_dataset('stop_time', 4); 37 | 38 | % for i in range(len(tags)-1): 39 | % epoch2.add_tag(tags[i]) 40 | epoch2.set_dataset('tags', tags(1:2)); 41 | 42 | f.close() 43 | 44 | % this test modified because tags are stored as dataset rather than attribute 45 | % tags = ut.verify_attribute_present(fname, 'epochs/epoch-1', 'tags'); 46 | stored_tags = test_utils.verify_present(fname, 'epochs/epoch-1', 'tags'); 47 | for i = 2:length(tags) 48 | if ~any(strcmp(tags(i), stored_tags)) 49 | test_utils.error('Verifying epoch tag content', 'epoch-1: all tags not present') 50 | end 51 | end 52 | 53 | % tags = ut.verify_attribute_present(fname, 'epochs/epoch-2', 'tags'); 54 | stored_tags = test_utils.verify_present(fname, 'epochs/epoch-2', 'tags'); 55 | for i = 1:length(tags)-1 % in range(len(tags)-1): 56 | if ~any(strcmp(tags(i), stored_tags)) % tags[i] not in tags: 57 | test_utils.error('Verifying epoch tag content', 'epoch-2: all tags not present') 58 | end 59 | end 60 | 61 | stored_tags = test_utils.verify_attribute_present(fname, 'epochs', 'tags'); 62 | for i = 1:length(tags) % in range(len(tags)): 63 | if ~any(strcmp(tags(i), stored_tags)) % tags[i] not in tags: 64 | test_utils.error('Verifying epoch tag content', 'epoch-3: all tags not present') 65 | end 66 | end 67 | 68 | 69 | fprintf('%s PASSED\n', script_name); 70 | end 71 | 72 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_general_opto.m: -------------------------------------------------------------------------------- 1 | function t_general_opto(verbosity) 2 | 3 | % TESTS fields stored in general/optogenetics 4 | 5 | script_base_name = mfilename(); 6 | script_name = [script_base_name '.m']; 7 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 8 | if nargin < 1 9 | % default, display all information. Other options are: 'none', 'summary' 10 | verbosity = 'all'; 11 | end 12 | 13 | 14 | function test_field(fname, name, subdir) 15 | val = test_utils.verify_present(fname, ['general/optogenetics/', subdir, '/'], lower(name)); 16 | if ~strcmp(val, name) 17 | test_utils.error('Checking metadata', 'field value incorrect'); 18 | end 19 | end 20 | 21 | 22 | function test_general_optogen() 23 | create_general_optogen(fname) 24 | % 25 | val = test_utils.verify_present(fname, 'general/optogenetics/', 'optogen_custom'); 26 | if ~strcmp(val, 'OPTOGEN_CUSTOM') 27 | test_utils.error('Checking custom', 'Field value incorrect') 28 | end 29 | % 30 | 31 | test_field(fname, 'DESCRIPTION', 'p1'); 32 | %test_field(fname, 'DESCRIPTIONx', 'p1') 33 | %test_field(fname, 'DESCRIPTION', 'p1x') 34 | test_field(fname, 'DEVICE', 'p1'); 35 | % test_field(fname, 'LAMBDA', 'p1') 36 | test_field(fname, 'EXCITATION_LAMBDA', 'p1'); 37 | test_field(fname, 'LOCATION', 'p1'); 38 | val = test_utils.verify_present(fname, 'general/optogenetics/p1/', 'optogen_site_custom'); 39 | if ~strcmp(val, 'OPTOGEN_SITE_CUSTOM') 40 | test_utils.error('Checking metadata', 'field value incorrect') 41 | end 42 | end 43 | 44 | 45 | function create_general_optogen(fname) 46 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 47 | 'identifier', nwb_utils.create_identifier('metadata optogenetic test'), ... 48 | 'description','test elements in /general/optogentics'}; 49 | f = nwb_file(settings{:}); 50 | 51 | % neurodata.set_metadata(OPTOGEN_CUSTOM('optogen_custom'), 'OPTOGEN_CUSTOM') 52 | % % 53 | % neurodata.set_metadata(OPTOGEN_SITE_DESCRIPTION('p1'), 'DESCRIPTION') 54 | % neurodata.set_metadata(OPTOGEN_SITE_DEVICE('p1'), 'DEVICE') 55 | % neurodata.set_metadata(OPTOGEN_SITE_LAMBDA('p1'), 'LAMBDA') 56 | % neurodata.set_metadata(OPTOGEN_SITE_LOCATION('p1'), 'LOCATION') 57 | % neurodata.set_metadata(OPTOGEN_SITE_CUSTOM('p1', 'optogen_site_custom'), 'OPTOGEN_SITE_CUSTOM') 58 | % 59 | 60 | g = f.make_group('optogenetics'); 61 | g.set_custom_dataset('optogen_custom', 'OPTOGEN_CUSTOM'); 62 | 63 | p1 = g.make_group('', 'p1'); 64 | p1.set_dataset('description','DESCRIPTION'); 65 | p1.set_dataset('device', 'DEVICE'); 66 | p1.set_dataset('excitation_lambda','EXCITATION_LAMBDA'); 67 | p1.set_dataset('location', 'LOCATION'); 68 | p1.set_custom_dataset('optogen_site_custom', 'OPTOGEN_SITE_CUSTOM'); 69 | 70 | % neurodata.close() 71 | f.close() 72 | end 73 | 74 | test_general_optogen() 75 | fprintf('%s PASSED\n', script_name); 76 | end 77 | 78 | 79 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_general_species.m: -------------------------------------------------------------------------------- 1 | function t_general_species(verbosity) 2 | 3 | % TESTS fields stored in general/subject 4 | 5 | script_base_name = mfilename(); 6 | script_name = [script_base_name '.m']; 7 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 8 | if nargin < 1 9 | % default, display all information. Other options are: 'none', 'summary' 10 | verbosity = 'all'; 11 | end 12 | 13 | function test_field(fname, name) 14 | val = test_utils.verify_present(fname, 'general/subject/', lower(name)); 15 | if ~strcmp(val, name) 16 | test_utils.error('Checking metadata', 'field value incorrect'); 17 | end 18 | end 19 | 20 | function test_general_subject() 21 | create_general_subject(fname); 22 | val = test_utils.verify_present(fname, 'general/subject/', 'description'); 23 | if ~strcmp(val, 'SUBJECT') 24 | ut.error('Checking metadata', 'field value incorrect') 25 | end 26 | test_field(fname, 'SUBJECT_ID'); 27 | test_field(fname, 'SPECIES'); 28 | test_field(fname, 'GENOTYPE'); 29 | test_field(fname, 'SEX'); 30 | test_field(fname, 'AGE'); 31 | test_field(fname, 'WEIGHT'); 32 | end 33 | 34 | 35 | function create_general_subject(fname) 36 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 37 | 'identifier', nwb_utils.create_identifier('general subject test'), ... 38 | 'description','test elements in /general/subject'}; 39 | f = nwb_file(settings{:}); 40 | 41 | % 42 | % neurodata.set_metadata(SUBJECT, 'SUBJECT') 43 | % neurodata.set_metadata(SUBJECT_ID, 'SUBJECT_ID') 44 | % neurodata.set_metadata(SPECIES, 'SPECIES') 45 | % neurodata.set_metadata(GENOTYPE, 'GENOTYPE') 46 | % neurodata.set_metadata(SEX, 'SEX') 47 | % neurodata.set_metadata(AGE, 'AGE') 48 | % neurodata.set_metadata(WEIGHT, 'WEIGHT') 49 | % 50 | 51 | g = f.make_group('subject'); 52 | g.set_dataset('description', 'SUBJECT'); 53 | g.set_dataset('subject_id', 'SUBJECT_ID'); 54 | g.set_dataset('species', 'SPECIES'); 55 | g.set_dataset('genotype', 'GENOTYPE'); 56 | g.set_dataset('sex', 'SEX'); 57 | g.set_dataset('age', 'AGE'); 58 | g.set_dataset('weight', 'WEIGHT'); 59 | 60 | % neurodata.close() 61 | f.close() 62 | end 63 | 64 | test_general_subject() 65 | fprintf('%s PASSED\n', script_name); 66 | end 67 | 68 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_general_top.m: -------------------------------------------------------------------------------- 1 | function t_general_top(verbosity) 2 | 3 | 4 | % TESTS top-level fields stored in general 5 | % TESTS storing metadata from file 6 | % TESTS 'Custom' tagging on custom attributes 7 | 8 | script_base_name = mfilename(); 9 | script_name = [script_base_name '.m']; 10 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 11 | if nargin < 1 12 | % default, display all information. Other options are: 'none', 'summary' 13 | verbosity = 'all'; 14 | end 15 | 16 | 17 | function test_field(fname, name) 18 | val = test_utils.verify_present(fname, 'general/', lower(name)); 19 | if ~strcmp(val, name) 20 | test_utils.error('Checking metadata', 'field value incorrect'); 21 | end 22 | end 23 | 24 | function test_general_top() 25 | create_general_top(fname) 26 | test_field(fname, 'DATA_COLLECTION'); 27 | test_field(fname, 'EXPERIMENT_DESCRIPTION'); 28 | test_field(fname, 'EXPERIMENTER'); 29 | test_field(fname, 'INSTITUTION'); 30 | test_field(fname, 'LAB'); 31 | test_field(fname, 'NOTES'); 32 | test_field(fname, 'PROTOCOL'); 33 | test_field(fname, 'PHARMACOLOGY'); 34 | test_field(fname, 'RELATED_PUBLICATIONS'); 35 | test_field(fname, 'SESSION_ID'); 36 | test_field(fname, 'SLICES'); 37 | test_field(fname, 'STIMULUS'); 38 | test_field(fname, 'SURGERY'); 39 | test_field(fname, 'VIRUS'); 40 | val = test_utils.verify_present(fname, 'general/', 'source_script'); 41 | if length(val) < 1000 42 | test_utils.error('Checking metadata_from_file', 'unexpected field size') 43 | end 44 | end 45 | 46 | % removing test for neurodata_type attribute custom on general/source_script, since its 47 | % not custom anymore 48 | % val = ut.verify_attribute_present(fname, 'general/source_script', 'neurodata_type') 49 | % if val != 'Custom' and val != b'Custom': 50 | % ut.error('Checking custom tag', 'neurodata_type incorrect') 51 | 52 | 53 | function create_general_top(fname) 54 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 55 | 'identifier', nwb_utils.create_identifier('general top test'), ... 56 | 'description','test top-level elements in /general'}; 57 | f = nwb_file(settings{:}); 58 | 59 | % neurodata.set_metadata(DATA_COLLECTION, 'DATA_COLLECTION') 60 | % neurodata.set_metadata(EXPERIMENT_DESCRIPTION, 'EXPERIMENT_DESCRIPTION') 61 | % neurodata.set_metadata(EXPERIMENTER, 'EXPERIMENTER') 62 | % neurodata.set_metadata(INSTITUTION, 'INSTITUTION') 63 | % neurodata.set_metadata(LAB, 'LAB') 64 | % neurodata.set_metadata(NOTES, 'NOTES') 65 | % neurodata.set_metadata(PROTOCOL, 'PROTOCOL') 66 | % neurodata.set_metadata(PHARMACOLOGY, 'PHARMACOLOGY') 67 | % neurodata.set_metadata(RELATED_PUBLICATIONS, 'RELATED_PUBLICATIONS') 68 | % neurodata.set_metadata(SESSION_ID, 'SESSION_ID') 69 | % neurodata.set_metadata(SLICES, 'SLICES') 70 | % neurodata.set_metadata(STIMULUS, 'STIMULUS') 71 | % neurodata.set_metadata(SURGERY, 'SURGERY') 72 | % neurodata.set_metadata(VIRUS, 'VIRUS') 73 | % % 74 | % neurodata.set_metadata_from_file('source_script', __file__) 75 | % 76 | 77 | f.set_dataset('data_collection','DATA_COLLECTION'); 78 | f.set_dataset('experiment_description','EXPERIMENT_DESCRIPTION'); 79 | f.set_dataset('experimenter','EXPERIMENTER'); 80 | f.set_dataset('institution','INSTITUTION'); 81 | f.set_dataset('lab','LAB'); 82 | f.set_dataset('notes','NOTES'); 83 | f.set_dataset('protocol','PROTOCOL'); 84 | f.set_dataset('pharmacology','PHARMACOLOGY'); 85 | f.set_dataset('related_publications', 'RELATED_PUBLICATIONS'); 86 | f.set_dataset('session_id','SESSION_ID'); 87 | f.set_dataset('slices','SLICES'); 88 | f.set_dataset('stimulus','STIMULUS'); 89 | f.set_dataset('surgery','SURGERY'); 90 | f.set_dataset('virus', 'VIRUS'); 91 | 92 | % f.neurodata.set_metadata_from_file('source_script', __file__) 93 | f.set_dataset('source_script', nwb_utils.load_file(script_name)); 94 | 95 | % neurodata.close() 96 | f.close() 97 | end 98 | 99 | test_general_top() 100 | fprintf('%s PASSED\n', script_name); 101 | end 102 | 103 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_if_add_ts.m: -------------------------------------------------------------------------------- 1 | function t_if_add_ts(verbosity) 2 | 3 | % test opening file in append mode 4 | % TESTS creating a module 5 | % TESTS creating an interface 6 | % TESTS adding a timeseries to an interface 7 | 8 | script_base_name = mfilename(); 9 | script_name = [script_base_name '.m']; 10 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 11 | if nargin < 1 12 | % default, display all information. Other options are: 'none', 'summary' 13 | verbosity = 'all'; 14 | end 15 | 16 | 17 | function test_file() 18 | create_iface_series(fname, true); 19 | name1 = 'Ones'; 20 | test_utils.verify_timeseries(fname, name1, 'processing/test module/BehavioralEvents', 'TimeSeries') 21 | end 22 | 23 | 24 | function create_iface_series(fname, newfile) 25 | if newfile 26 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 27 | 'start_time', 'Sat Jul 04 2015 3:14:16' ... 28 | 'identifier', nwb_utils.create_identifier('interface timeseries example'), ... 29 | 'description','Test interface timeseries file'}; 30 | else 31 | settings = {'file_name', fname, 'mode', 'r+'}; 32 | end 33 | f = nwb_file(settings{:}); 34 | 35 | % 36 | % mod = neurodata.create_module('test module') 37 | % iface = mod.create_interface('BehavioralEvents') 38 | % ts = neurodata.create_timeseries('TimeSeries', 'Ones') 39 | % ts.set_data(np.ones(10), unit='Event', conversion=1.0, resolution=float('nan')) 40 | % ts.set_value('num_samples', 10) 41 | % ts.set_time(np.arange(10)) 42 | % iface.add_timeseries(ts) 43 | % iface.finalize() 44 | % mod.finalize() 45 | 46 | 47 | mod = f.make_group('', 'test module'); 48 | iface = mod.make_group('BehavioralEvents'); 49 | ts = iface.make_group('', 'Ones'); 50 | ts.set_dataset('data', ones([1, 10]), 'attrs', {'unit', 'Event', ... 51 | 'conversion', 1.0, 'resolution', NaN}); 52 | ts.set_dataset('num_samples', 10); 53 | ts.set_dataset('timestamps',0:9); 54 | 55 | % 56 | % neurodata.close() 57 | f.close() 58 | end 59 | 60 | test_file() 61 | fprintf('%s PASSED\n', script_name); 62 | end 63 | 64 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_modification_time.m: -------------------------------------------------------------------------------- 1 | function t_modification_time(verbosity) 2 | 3 | % creates file and modifies it multiple times 4 | 5 | script_base_name = mfilename(); 6 | script_name = [script_base_name '.m']; 7 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 8 | if nargin < 1 9 | % default, display all information. Other options are: 'none', 'summary' 10 | verbosity = 'all'; 11 | end 12 | 13 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 14 | 'start_time', 'Sat Jul 04 2015 3:14:16' ... 15 | 'identifier', nwb_utils.create_identifier('Modification example'), ... 16 | 'description','Modified empty file'}; 17 | 18 | f = nwb_file(settings{:}); 19 | f.close() 20 | 21 | 22 | settings = {'file_name', fname, 'mode', 'r+', 'verbosity', verbosity}; 23 | f = nwb_file(settings{:}); 24 | % need to change the file for SLAPI to update file_create_date 25 | f.set_dataset('species', 'SPECIES'); 26 | f.close() 27 | 28 | 29 | settings = {'file_name', fname, 'mode', 'r+', 'verbosity', verbosity}; 30 | f = nwb_file(settings{:}); 31 | % need to change the file for SLAPI to update file_create_date 32 | f.set_dataset('genotype', 'GENOTYPE'); 33 | f.close() 34 | 35 | % read data using matlab hdf5 api 36 | dates = hdf5read(fname,'file_create_date'); 37 | % f = py.h5py.File(fname); 38 | % dates = f['file_create_date'] 39 | if length(dates) ~= 3 40 | test_utils.error(filename, sprintf('Expected 3 entries in file_create_date; found %d', length(dates))) 41 | end 42 | 43 | fprintf('%s PASSED\n', script_name); 44 | end 45 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_no_data.m: -------------------------------------------------------------------------------- 1 | function t_no_data(verbosity) 2 | 3 | % creates time series without 'data' field 4 | % TESTS TimeSeries.ignore_data() 5 | 6 | script_base_name = mfilename(); 7 | script_name = [script_base_name '.m']; 8 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 9 | if nargin < 1 10 | % default, display all information. Other options are: 'none', 'summary' 11 | verbosity = 'all'; 12 | end 13 | 14 | 15 | function test_nodata_series() 16 | name = 'nodata'; 17 | % create_nodata_series(fname, name, 'acquisition') 18 | create_nodata_series(fname, name, '/acquisition/timeseries'); 19 | test_utils.verify_timeseries(fname, name, 'acquisition/timeseries', 'TimeSeries'); 20 | test_utils.verify_absent(fname, ['acquisition/timeseries/', name], 'data'); 21 | end 22 | 23 | function create_nodata_series(fname, name, target) 24 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity ... 25 | 'start_time', 'Sat Jul 04 2015 3:14:16' ... 26 | 'identifier', nwb_utils.create_identifier('nodata example'), ... 27 | 'description','time series no data test'}; 28 | f = nwb_file(settings{:}); 29 | nodata = f.make_group('', name, 'path', target); 30 | nodata.set_dataset('timestamps', {0}); % use cell array to create 1 element array 31 | f.close() 32 | end 33 | 34 | test_nodata_series() 35 | fprintf('%s PASSED\n', script_name); 36 | end 37 | 38 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_no_time.m: -------------------------------------------------------------------------------- 1 | function t_no_time(verbosity) 2 | 3 | % creates time series without 'timestamps' or 'starting_time' fields 4 | % TESTS TimeSeries.ignore_time() 5 | % TESTS timeseries placement in acquisition, stimulus, templates 6 | 7 | script_base_name = mfilename(); 8 | script_name = [script_base_name '.m']; 9 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 10 | if nargin < 1 11 | % default, display all information. Other options are: 'none', 'summary' 12 | verbosity = 'all'; 13 | end 14 | 15 | function test_notime_series() 16 | name = 'notime'; 17 | % create_notime_series(fname, name, 'acquisition') 18 | create_notime_series(fname, name, '/acquisition/timeseries') 19 | test_utils.verify_timeseries(fname, name, 'acquisition/timeseries', 'TimeSeries') 20 | test_utils.verify_absent(fname, ['acquisition/timeseries/',name], 'timestamps') 21 | test_utils.verify_absent(fname, ['acquisition/timeseries/',name], 'starting_time') 22 | 23 | % create_notime_series(fname, name, 'stimulus') 24 | create_notime_series(fname, name, '/stimulus/presentation') 25 | test_utils.verify_timeseries(fname, name, 'stimulus/presentation', 'TimeSeries') 26 | % create_notime_series(fname, name, 'template') 27 | create_notime_series(fname, name, '/stimulus/templates') 28 | test_utils.verify_timeseries(fname, name, 'stimulus/templates', 'TimeSeries') 29 | end 30 | 31 | function create_notime_series(fname, name, target) 32 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 33 | 'start_time', 'Sat Jul 04 2015 3:14:16' ... 34 | 'identifier', nwb_utils.create_identifier('notime example'), ... 35 | 'description','Test no time'}; 36 | f = nwb_file(settings{:}); 37 | 38 | notime = f.make_group('', name, 'path', target); 39 | % following used for testing more missing_fields 40 | % notime = f.make_group('', name, path=target) 41 | % not sure why cell array used below. Maybe required if only one 42 | % element 43 | notime.set_dataset('data', {0.0}, 'attrs', {'unit', 'n/a', ... 44 | 'conversion', 1.0, 'resolution', 1.0}); 45 | f.close() 46 | end 47 | 48 | test_notime_series() 49 | fprintf('%s PASSED\n', script_name); 50 | end 51 | 52 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_ref_image.m: -------------------------------------------------------------------------------- 1 | function t_ref_image(verbosity) 2 | 3 | % TESTS storage of reference image 4 | 5 | script_base_name = mfilename(); 6 | script_name = [script_base_name '.m']; 7 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 8 | if nargin < 1 9 | % default, display all information. Other options are: 'none', 'summary' 10 | verbosity = 'all'; 11 | end 12 | 13 | 14 | function test_refimage_series() 15 | name = 'refimage'; 16 | create_refimage(fname, name) 17 | val = test_utils.verify_present(fname, 'acquisition/images/', name); 18 | %if len(val) != 6: 19 | if length(val) ~= 5 20 | test_utils.error('Checking ref image contents', 'wrong dimension') 21 | end 22 | val = test_utils.verify_attribute_present(fname, ['acquisition/images/', name], 'format'); 23 | if ~strcmp(val, 'raw') 24 | test_utils.error('Checking ref image format', 'Wrong value') 25 | end 26 | val = test_utils.verify_attribute_present(fname, ['acquisition/images/',name], 'description'); 27 | if ~strcmp(val, 'test') 28 | test_utils.error('Checking ref image description', 'Wrong value') 29 | end 30 | end 31 | 32 | function create_refimage(fname, name) 33 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 34 | 'start_time', 'Sat Jul 04 2015 3:14:16' ... 35 | 'identifier', nwb_utils.create_identifier('reference image test'), ... 36 | 'description','reference image test'}; 37 | f = nwb_file(settings{:}); 38 | 39 | % neurodata.create_reference_image([1,2,3,4,5], name, 'raw', 'test') 40 | f.set_dataset('', [1,2,3,4,5], 'dtype', 'uint8', 'name', name, 'attrs', { ... 41 | 'description', 'test', 'format', 'raw'}); 42 | 43 | f.close() 44 | end 45 | 46 | test_refimage_series() 47 | fprintf('%s PASSED\n', script_name); 48 | end 49 | 50 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_softlink.m: -------------------------------------------------------------------------------- 1 | function t_softlink(verbosity) 2 | 3 | % creates time series without 'data' field 4 | % TESTS softlink of TimeSeries.data 5 | 6 | script_base_name = mfilename(); 7 | script_name = [script_base_name '.m']; 8 | fname1 = [regexprep(script_base_name, '^t_', 's_') '1.nwb']; 9 | fname2 = [regexprep(script_base_name, '^t_', 's_') '2.nwb']; 10 | if nargin < 1 11 | % default, display all information. Other options are: 'none', 'summary' 12 | verbosity = 'all'; 13 | end 14 | 15 | function test_softlink() 16 | name1 = 'softlink_source'; 17 | name2 = 'softlink_reader'; 18 | % create_softlink_source(fname1, name1, 'acquisition') 19 | % create_softlink_reader(fname2, name2, fname1, name1, 'acquisition') 20 | create_softlink_source(fname1, name1, '/acquisition/timeseries'); 21 | create_softlink_reader(fname2, name2, fname1, name1, '/acquisition/timeseries'); 22 | % 23 | test_utils.verify_timeseries(fname1, name1, 'acquisition/timeseries', 'TimeSeries'); 24 | test_utils.verify_timeseries(fname2, name2, 'acquisition/timeseries', 'TimeSeries'); 25 | % 26 | val = test_utils.verify_present(fname2, ['acquisition/timeseries/', name2], 'data'); 27 | end 28 | 29 | 30 | function create_softlink_reader(fname, name, src_fname, src_name, target) 31 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 32 | 'start_time', 'Sat Jul 04 2015 3:14:16' ... 33 | 'identifier', nwb_utils.create_identifier('softlink reader'), ... 34 | 'description','softlink test'}; 35 | f = nwb_file(settings{:}); 36 | 37 | % source = neurodata.create_timeseries('TimeSeries', name, target) 38 | % source.set_data_as_remote_link(src_fname, 'acquisition/timeseries/'+src_name+'/data') 39 | % source.set_time([345]) 40 | % source.finalize() 41 | % neurodata.close() 42 | 43 | source = f.make_group('', name, 'path', target); 44 | % source.set_data_as_remote_link(src_fname, 'acquisition/timeseries/'+src_name+'/data') 45 | extlink = sprintf('extlink:%s,%s', src_fname, ['acquisition/timeseries/', src_name, '/data']); 46 | source.set_dataset('data', extlink); 47 | source.set_dataset('timestamps', {345}); % put in cell array to make array in hdf5 file 48 | % source.finalize() 49 | % neurodata.close() 50 | f.close() 51 | end 52 | 53 | function create_softlink_source(fname, name, target) 54 | 55 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 56 | 'start_time', 'Sat Jul 04 2015 3:14:16' ... 57 | 'identifier', nwb_utils.create_identifier('softlink source'), ... 58 | 'description','time series no data test'}; 59 | f = nwb_file(settings{:}); 60 | % source = neurodata.create_timeseries('TimeSeries', name, target) 61 | source = f.make_group('', name, 'path', target); 62 | % source.set_data([234], unit='parsec', conversion=1, resolution=1e-3) 63 | source.set_dataset('data', {234.0}, 'attrs', {'unit', 'parsec', ... 64 | 'conversion', 1.0, 'resolution', 1e-3}); 65 | % source.set_time([123]) 66 | source.set_dataset('timestamps', {123.0}); 67 | % source.finalize() 68 | % neurodata.close() 69 | f.close() 70 | end 71 | 72 | test_softlink() 73 | fprintf('%s PASSED\n', script_name); 74 | end 75 | 76 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_starting_time.m: -------------------------------------------------------------------------------- 1 | function t_starting_time(verbosity) 2 | 3 | % TESTS use of TimeSeries.starting_time 4 | 5 | script_base_name = mfilename(); 6 | script_name = [script_base_name '.m']; 7 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 8 | if nargin < 1 9 | % default, display all information. Other options are: 'none', 'summary' 10 | verbosity = 'all'; 11 | end 12 | 13 | function test_nodata_series() 14 | name = 'starting_time'; 15 | % create_startingtime_series(fname, name, 'acquisition') 16 | create_startingtime_series(fname, name, '/acquisition/timeseries'); 17 | test_utils.verify_timeseries(fname, name, 'acquisition/timeseries', 'TimeSeries'); 18 | test_utils.verify_absent(fname, ['acquisition/timeseries/', name], 'timestamps'); 19 | val = test_utils.verify_present(fname, ['acquisition/timeseries/', name], 'starting_time'); 20 | if val ~= 0.125 21 | test_utils.error('Checking start time', 'Incorrect value') 22 | end 23 | val = test_utils.verify_attribute_present(fname, ['acquisition/timeseries/starting_time/', name], 'rate'); 24 | if val ~= 2 25 | test_utils.error('Checking rate', 'Incorrect value') 26 | end 27 | end 28 | 29 | function create_startingtime_series(fname, name, target) 30 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 31 | 'start_time', 'Sat Jul 04 2015 3:14:16' ... 32 | 'identifier', nwb_utils.create_identifier('starting time test'), ... 33 | 'description','time series starting time test'}; 34 | f = nwb_file(settings{:}); 35 | 36 | % 37 | % stime = neurodata.create_timeseries('TimeSeries', name, target) 38 | % stime.set_data([0, 1, 2, 3], unit='n/a', conversion=1, resolution=1) 39 | % stime.set_value('num_samples', 4) 40 | % stime.set_time_by_rate(0.125, 2) 41 | % 42 | 43 | stime = f.make_group('', name, 'path', target); 44 | stime.set_dataset('data', [0.0, 1.0, 2.0, 3.0], 'attrs', {'unit', 'n/a', ... 45 | 'conversion', 1.0, 'resolution', 1.0}); 46 | stime.set_dataset('num_samples', 4); 47 | 48 | % stime.set_time_by_rate(0.125, 2) 49 | stime.set_dataset('starting_time', 0.125, 'attrs', {'rate', 2.0, 'unit', 'Seconds'}); 50 | % stime.finalize() 51 | % neurodata.close() 52 | f.close() 53 | end 54 | 55 | test_nodata_series() 56 | fprintf('%s PASSED\n', script_name); 57 | end 58 | 59 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_top_datasets.m: -------------------------------------------------------------------------------- 1 | function t_top_datasets(verbosity) 2 | 3 | script_base_name = mfilename(); 4 | script_name = [script_base_name '.m']; 5 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 6 | if nargin < 1 7 | % default, display all information. Other options are: 'none', 'summary' 8 | verbosity = 'all'; 9 | end 10 | 11 | % TESTS top-level datasets 12 | 13 | function test_refimage_series() 14 | name = 'refimage'; 15 | create_refimage(fname, name) 16 | val = test_utils.verify_present(fname, '/', 'identifier'); 17 | if ~strcmp(val, 'vwx') 18 | test_utils.error('Checking file idenfier', 'wrong contents') 19 | end 20 | val = test_utils.verify_present(fname, '/', 'file_create_date'); 21 | val = test_utils.verify_present(fname, '/', 'session_start_time'); 22 | if ~strcmp(val, 'xyz') 23 | test_utils.error('Checking session start time', 'wrong contents') 24 | end 25 | val = test_utils.verify_present(fname, '/', 'session_description'); 26 | if ~strcmp(val, 'wxy') 27 | test_utils.error('Checking session start time', 'wrong contents') 28 | end 29 | end 30 | 31 | function create_refimage(fname, name) 32 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 33 | 'start_time', 'xyz' ... 34 | 'identifier', 'vwx', ... 35 | 'description','wxy'}; 36 | f = nwb_file(settings{:}); 37 | f.close() 38 | end 39 | 40 | test_refimage_series() 41 | fprintf('%s PASSED\n', script_name); 42 | end 43 | 44 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/t_unittimes.m: -------------------------------------------------------------------------------- 1 | function t_unittimes(verbosity) 2 | 3 | % TESTS creation of UnitTimes interface and data stored within 4 | 5 | script_base_name = mfilename(); 6 | script_name = [script_base_name '.m']; 7 | fname = [regexprep(script_base_name, '^t_', 's_') '.nwb']; 8 | if nargin < 1 9 | % default, display all information. Other options are: 'none', 'summary' 10 | verbosity = 'all'; 11 | end 12 | 13 | function test_unit_times() 14 | % create the file we're going to use 15 | ndata = create_empty_file(fname); 16 | % create a module to store processed data 17 | % mod = ndata.create_module('my spike times') 18 | mod = ndata.make_group('', 'my spike times'); 19 | % ad a unit times interface to the module 20 | % iface = mod.create_interface('UnitTimes') 21 | iface = mod.make_group('UnitTimes'); 22 | % make some data to store 23 | spikes = create_spikes(); 24 | % for i in range(len(spikes)): 25 | % iface.add_unit(unit_name = 'unit-%d' % i, 26 | % unit_times = spikes[i], 27 | % description = '', 28 | % source = 'Data spike-sorted by B. Bunny') 29 | 30 | for i = 1:length(spikes) % range(len(spikes)): 31 | unit_name = sprintf('unit-%d', i-1); 32 | ug = iface.make_group('', unit_name); 33 | ug.set_dataset('times', spikes{i}); 34 | ug.set_dataset('unit_description', ''); 35 | ug.set_dataset('source', 'Data spike-sorted by B. Bunny'); 36 | end 37 | 38 | 39 | % clean up and close objects 40 | % iface.finalize() 41 | % mod.finalize() 42 | ndata.close() 43 | 44 | % test random sample to make sure data was stored correctly 45 | % h5 = h5py.File(fname) 46 | % times = h5['processing/my spike times/UnitTimes/unit-0/times'].value 47 | % assert len(times) == len(spikes[0]), 'Spike count for unit-0 wrong' 48 | % assert abs(times[1] - spikes[0][1]) < 0.001, 'Wrong time found in file' 49 | % h5.close() 50 | times = hdf5read(fname,'processing/my spike times/UnitTimes/unit-0/times'); 51 | if length(times) ~= length(spikes{1}) 52 | error('Spike count for unit-0 wrong') 53 | end 54 | if abs(times(2) - spikes{1}(2)) >= 0.001 55 | error('Wrong time found in file') 56 | end 57 | end 58 | 59 | 60 | function [spikes] = create_spikes() 61 | spikes = cell([1, 3]); 62 | spikes{1} = [1.3, 1.4, 1.9, 2.1, 2.2, 2.3]; 63 | spikes{2} = [2.2, 3.0]; 64 | spikes{3} = [0.3, 0.4, 1.0, 1.1, 1.45, 1.8, 1.81, 2.2]; 65 | end 66 | 67 | 68 | function [f] = create_empty_file(fname) 69 | settings = {'file_name', fname, 'mode', 'w', 'verbosity', verbosity, ... 70 | 'start_time', 'Sat Jul 04 2015 3:14:16' ... 71 | 'identifier', nwb_utils.create_identifier('UnitTimes example'), ... 72 | 'description','Test file with spike times in processing module'}; 73 | f = nwb_file(settings{:}); 74 | end 75 | 76 | test_unit_times() 77 | fprintf('%s PASSED\n', script_name); 78 | end 79 | 80 | -------------------------------------------------------------------------------- /matlab_bridge/matlab_unittest/test_utils.m: -------------------------------------------------------------------------------- 1 | classdef test_utils 2 | % Utility functions for matlab unit tests 3 | % These call the functions in Python file test_utils.py 4 | 5 | properties 6 | end 7 | 8 | methods(Static) 9 | function error(context, err_string) 10 | py.test_utils.error(context, err_string); 11 | end 12 | function [val] = verify_present(hfile, group, field) 13 | pval = py.test_utils.verify_present(hfile, group, field); 14 | val = nwb_utils.convert_py_data(pval); 15 | end 16 | function [val] = verify_attribute_present(hfile, obj, field) 17 | pval = py.test_utils.verify_attribute_present(hfile, obj, field); 18 | val = nwb_utils.convert_py_data(pval); 19 | end 20 | function verify_timeseries(hfile, name, location, ts_type) 21 | py.test_utils.verify_timeseries(hfile, name, location, ts_type); 22 | end 23 | function verify_absent(hfile, group, field) 24 | py.test_utils.verify_absent(hfile, group, field); 25 | end 26 | function [match] = search_for_substring(h5_str, value) 27 | if iscell(h5_str) 28 | % convert cell array to list 29 | h5_str = py.list(h5_str); 30 | end 31 | match = py.test_utils.search_for_substring(h5_str, value); 32 | end 33 | 34 | % function [cellP] = list2cell(pylist) 35 | % % convert python list of strings to cell array 36 | % cP = cell(pylist); 37 | % cellP = cell(1, numel(cP)); 38 | % for n = 1:numel(cP) 39 | % strP = char(cP{n}); 40 | % cellP(n) = {strP}; 41 | % end 42 | % end 43 | end 44 | end 45 | 46 | -------------------------------------------------------------------------------- /nwb/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NeurodataWithoutBorders/api-python/52e97e7642021913ae6505ab63b7cc77d2622d76/nwb/__init__.py -------------------------------------------------------------------------------- /nwb/check_schema.py: -------------------------------------------------------------------------------- 1 | # script to validate h5gate schema files using json schema 2 | 3 | import os.path 4 | import sys 5 | # import json 6 | import jsonschema 7 | import ast 8 | 9 | def load_schema(file_name): 10 | """ Load Python file that contains JSON formatted as a Python dictionary. 11 | Files in this format are used to store the schema because, unlike pure JSON, 12 | they allow comments and formatting long strings to make them easier to read.""" 13 | if not os.path.isfile(file_name): 14 | print ("Unable to locate file %s" % file_name) 15 | sys.exit(1) 16 | f = open(file_name) 17 | file_contents = f.read() 18 | f.close() 19 | # 20 | # with file(file_name) as f: 21 | # file_contents = f.read() 22 | try: 23 | # use use ast.literal_eval to parse 24 | pydict = ast.literal_eval(file_contents) 25 | except Exception as e: 26 | print ("** Unable to parse file '%s' (should be mostly JSON)" % file_name) 27 | print ("Error is: %s" % e) 28 | sys.exit(1) 29 | assert isinstance(pydict, dict), "** File '%s does not contain python dictionary" % file_name 30 | return pydict 31 | 32 | 33 | def load_meta_schema(): 34 | meta_schema_file = "meta_schema.json" 35 | if not os.path.isfile(meta_schema_file): 36 | print ("Unable to locate file %s" % file_name) 37 | sys.exit(1) 38 | with file(meta_schema_file) as f: 39 | file_contents = f.read() 40 | meta_schema = json.loads(file_contents) 41 | return meta_schema 42 | 43 | 44 | if __name__ == "__main__": 45 | nwb_dir = os.path.dirname(os.path.realpath(__file__)) 46 | meta_schema_file = os.path.join(nwb_dir, "meta_schema.py") 47 | fs_var = "fs" 48 | if len(sys.argv) != 2: 49 | print ("format is:") 50 | print ("python %s " % sys.argv[0]) 51 | print ("where is either the name of a schema file, or '-' for the") 52 | print ("default core specification (nwb_core.py), or 'N' - to process the core specification") 53 | print ("but not display the full path to it (so output will not depend on the location") 54 | print ("NWB is installed in).") 55 | sys.exit(0) 56 | using_core = sys.argv[1] in ("-", "N") 57 | schema_file = os.path.join(nwb_dir, 'nwb_core.py') if using_core else sys.argv[1] 58 | filter_path = sys.argv[1] == "N" 59 | meta_schema = load_schema(meta_schema_file) 60 | schema = load_schema(schema_file) 61 | if fs_var not in schema: 62 | print ("** Error, key '%s' not defined in top level of file '%s'" % (fs_var, schema_file)) 63 | sys.exit(1) 64 | schema = schema[fs_var] 65 | display_name = ".../nwb/nwb_core.py" if filter_path else schema_file 66 | print ("checking specification in file '%s'" % display_name) 67 | jsonschema.validate(schema, meta_schema) 68 | print ("File is valid.") 69 | 70 | 71 | 72 | 73 | -------------------------------------------------------------------------------- /nwb/display_versions.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import os 3 | 4 | # Function to display Python and hdf5 version from both Python 5 | # and Python called from matlab 6 | 7 | # To run by calling Python directly, enter the following command into the 8 | # operating system shell: 9 | # python -m nwb.display_versions 10 | 11 | # To run from Matlab enter the following command into the Matlab command window: 12 | # py.nwb.display_versions.matlab() 13 | 14 | # The versions displayed by the above two calls should be the same. 15 | # If the output is different, you need to specify the 16 | # correct version of Python to Matlab as described in the 17 | # matlab_bridge 0_INSTALL.txt file. 18 | 19 | 20 | 21 | def display_versions(): 22 | print ("** environment variables:") 23 | for key in sorted(os.environ.keys()): 24 | print( "%s - %s" % (key, os.environ[key])) 25 | print ("** Versions:") 26 | print ("Python: %s" % sys.version) 27 | print ("Python executable: %s" % sys.executable) 28 | try: 29 | import h5py 30 | except: 31 | e = sys.exc_info()[0] 32 | print ("unable to import hd5f: %s" % e) 33 | else: 34 | print ("HDF5 API: %s" % h5py.version.api_version) 35 | print ("HDF5: %s" % h5py.version.hdf5_version) 36 | 37 | def matlab(): 38 | print ("\n**** called from MatLab") 39 | display_versions() 40 | 41 | 42 | if __name__ == "__main__": 43 | print ("\n**** called directly from Python") 44 | display_versions() 45 | -------------------------------------------------------------------------------- /nwb/make_docs.py: -------------------------------------------------------------------------------- 1 | # program to generate documentation from specification language definition(s) 2 | 3 | import sys 4 | # h5gate validate script 5 | from . import h5gate as g 6 | from . import doc_tools as dt 7 | 8 | # print "sys.argv=%s" % sys.argv 9 | 10 | if len(sys.argv) < 1 or len(sys.argv) > 3: 11 | print ("format is:") 12 | print ("pyhton %s [ [] ]" % sys.argv[0]) 13 | print ("OR") 14 | print ("python %s ") 15 | print ("where:") 16 | print (" is a common separated list of extension files, or '-' for none") 17 | print (" is the core format specification file. Default is 'nwb_core.py'") 18 | print (" is an hdf5 (extension not '.py') containing format specifications") 19 | sys.exit(0) 20 | if len(sys.argv) == 2 and not sys.argv[1].endswith('.py'): 21 | # assume loading specifications from hdf5 file 22 | spec_files = [] 23 | file_name = sys.argv[1] 24 | else: 25 | core_spec = 'nwb_core.py' if len(sys.argv) < 3 else sys.argv[2] 26 | extensions = [] if len(sys.argv) < 2 or sys.argv[1] == '-' else sys.argv[1].split(',') 27 | spec_files = [core_spec] + extensions 28 | file_name = None 29 | options={'mode':'no_file'} 30 | f = g.File(file_name, spec_files, options=options) 31 | # doc = dt.generate(f) 32 | dt.build_node_tree(f) 33 | html = dt.make_doc(f) 34 | f.close() 35 | print (html) 36 | 37 | -------------------------------------------------------------------------------- /nwb/make_json.py: -------------------------------------------------------------------------------- 1 | 2 | # program to convert nwb_core.py specification language file to JSON 3 | # format 4 | 5 | import nwb_core 6 | import json 7 | 8 | json=json.dumps(nwb_core.nwb, indent=4, separators=(',', ': ')) 9 | f1=open('nwb_core.json', 'w') 10 | f1.write(json) 11 | -------------------------------------------------------------------------------- /nwb/nwb_init.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import nwb.nwb_utils as ut 3 | 4 | def nwb_init(f, mode, start_time, identifier, description, creating_file): 5 | """ Set initial metadata if creating a new file or set callback for 6 | updating modification time if modifying an existing file. f is the 7 | h5gate File object. creating_file is True if creating a new file. 8 | See file nwb_file for description of mode, start_time, identifier and 9 | description. 10 | """ 11 | if mode in ('r+', 'a') and not creating_file: 12 | # modifying existing file. Setup callback to update modification_time 13 | f.set_close_callback(nwb_close_callback) 14 | elif creating_file: 15 | # set initial metadata for new file 16 | version = f.ddef[f.default_ns]['info']['version'] 17 | # vinfo = ["Specification(s):"] 18 | # vinfo.append("file name\tnamespace\tversion\tdate") 19 | # for file_name in f.spec_files: 20 | # for ns in f.fsname2ns[file_name]: 21 | # version = f.ddef[ns]['info']['version'] 22 | # date = f.ddef[ns]['info']['date'] 23 | # info = "%s\t%s\t%s\t%s" % (file_name, ns, version, date) 24 | # vinfo.append(info) 25 | # vinfo.append("Default namespace='%s'" % f.default_ns) 26 | # api_version = f.get_version() 27 | # vinfo.append("API: %s" % api_version) 28 | # version = "\n".join(vinfo) 29 | f.set_dataset("nwb_version", version) 30 | f.set_dataset("identifier", identifier) 31 | f.set_dataset("session_description", description) 32 | curr_time = ut.current_time() 33 | f.set_dataset("file_create_date", [curr_time, ]) 34 | if not start_time: 35 | start_time = curr_time 36 | f.set_dataset("session_start_time", start_time) 37 | 38 | 39 | def nwb_close_callback(f): 40 | """ Executed on close of nwb file. Updates modification time""" 41 | if f.file_changed: 42 | if f.creating_file or f.options['mode'] not in ('r+', 'a'): 43 | print ("Unexpected condition when calling close_callback. " 44 | "creating_file=%s, mode=%s") %(f.creating_file, f.options['mode']) 45 | sys.exit(1) 46 | # file changed. Append current time to modification time 47 | cd = f.get_node("/file_create_date", abort = False) 48 | if not cd: 49 | f.warning.append("Unable to append modification time to /file_create_date. " 50 | " Dataset does not exist.") 51 | else: 52 | cur_time = ut.current_time() 53 | cd.append(cur_time) 54 | else: 55 | f.warning.append("Not updating modification time because file was not changed.") 56 | 57 | # Below code used if modifications_time stored as attribute 58 | # if "modification_time" in cd.h5attrs: 59 | # mod_times = cd.h5attrs["modification_time"] 60 | # if not isinstance(mod_times, (list,)): 61 | # f.warning.append("Did not update modification time, because type " 62 | # "was unexpected: %s") % type(mod_times) 63 | # else: 64 | # cur_time = utils.current_time() 65 | # mod_times = mod_times + [cur_time] # don't use append to avoid changing original 66 | # cd.set_attr("modification_time", mod_times) 67 | # print "Updated modification time.""" 68 | 69 | 70 | 71 | -------------------------------------------------------------------------------- /nwb/suggest_spellings.py: -------------------------------------------------------------------------------- 1 | 2 | # function get_possible_matches - used to return list of possible 3 | # matching words in a list if the word was supposed to be in the 4 | # list but not found, possibly due to a spelling error. 5 | # adapted from: 6 | # http://norvig.com/spell-correct.html 7 | 8 | 9 | alphabet = 'abcdefghijklmnopqrstuvwxyz' 10 | 11 | def edits1(word): 12 | splits = [(word[:i], word[i:]) for i in range(len(word) + 1)] 13 | deletes = [a + b[1:] for a, b in splits if b] 14 | transposes = [a + b[1] + b[0] + b[2:] for a, b in splits if len(b)>1] 15 | replaces = [a + c + b[1:] for a, b in splits for c in alphabet if b] 16 | inserts = [a + c + b for a, b in splits for c in alphabet] 17 | return set(deletes + transposes + replaces + inserts) 18 | 19 | def known_edits2(word, choices): 20 | return set(e2 for e1 in edits1(word) for e2 in edits1(e1) if e2 in choices) 21 | 22 | def known(words, choices): return set(w for w in words if w in choices) 23 | 24 | 25 | def get_possible_matches(word, choices): 26 | """ given word, that is not in list words, find possible matches based on 27 | edits. This used to generate list of possible matches in case there was a 28 | misspelling""" 29 | ch = set(choices) 30 | candidates = known(edits1(word), ch) or known_edits2(word, ch) 31 | return sorted(list(candidates)) 32 | 33 | 34 | def test_get_possible_matches(): 35 | choices = ["stimulus", "hippocampus", "mouse", "module", "interface"] 36 | words = ["stimuls", "hipppocampus", "mose", "modlue", "interfaces"] 37 | for word in words: 38 | possible_matches = get_possible_matches(word, choices) 39 | print ("%s found %s" % (word, possible_matches)) 40 | 41 | 42 | if __name__ == '__main__': 43 | test_get_possible_matches() 44 | -------------------------------------------------------------------------------- /nwb/validate.py: -------------------------------------------------------------------------------- 1 | 2 | # program to validate nwb files using specification language definition 3 | 4 | import sys 5 | import nwb.nwb_file as nwb_file 6 | # import cProfile # for profiling 7 | 8 | def validate_file(name, core_spec="nwb_core.py", extensions=None, verbosity="all"): 9 | """ 10 | Parameters 11 | ---------- 12 | name: string 13 | Name (including path) of file to be validated 14 | 15 | core_spec: string (default: 'nwb_core.py') 16 | Name of core specification file or '-' to load specification(s) from HDF5 file. 17 | 18 | extensions: array 19 | Array of extension files 20 | 21 | verbosity: string (default: 'all') 22 | Controls how much validation output is displayed. Options are: 23 | 'all', 'summary', and 'none' 24 | 25 | 26 | Returns 27 | ------- 28 | validation_result: dict 29 | Result of validation. Has keys: 'errors', 'warnings', 'added' which 30 | contain counts of errors, warnings and additions. Additions are groups, 31 | datasets or attributes added which are not defined by the core_spec 32 | specification. 33 | """ 34 | if extensions is None: 35 | extensions = [] 36 | # to validate, open the file in read-only mode, then close it 37 | f = nwb_file.open(name, mode="r", core_spec=core_spec, extensions=extensions, verbosity=verbosity) 38 | validation_result = f.close() 39 | return validation_result 40 | 41 | 42 | if __name__ == "__main__": 43 | 44 | if len(sys.argv) < 2 or len(sys.argv) > 4: 45 | print("format is:") 46 | print("python %s [ [] ]" % sys.argv[0]) 47 | print("where:") 48 | print(" is a common separated list of extension files, or '-' for none") 49 | print(" is the core format specification file. Default is 'nwb_core.py'") 50 | print("Use two dashes, e.g. '- -' to load saved specifications from ") 51 | sys.exit(0) 52 | core_spec = 'nwb_core.py' if len(sys.argv) < 4 else sys.argv[3] 53 | extensions = [] if len(sys.argv) < 3 or sys.argv[2] == '-' else sys.argv[2].split(',') 54 | file_name = sys.argv[1] 55 | if extensions == [] and core_spec == "-": 56 | print("Loading specifications from file '%s'" % file_name) 57 | validate_file(file_name, core_spec=core_spec, extensions=extensions) 58 | # replace above call with following to generate execution time profile 59 | # cProfile.run('validate_file("%s", core_spec="%s")' % (file_name, core_spec)) 60 | 61 | 62 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup 2 | # from distutils.core import setup 3 | 4 | setup( 5 | name = 'nwb', 6 | version = '1.0.6', 7 | url='https://github.com/NeurodataWithoutBorders/api-python', 8 | author='Jeff Teeters and Keith Godfrey', 9 | author_email='jteeters@berkeley.edu', 10 | description = 'Python API for Neurodata Without Borders (NWB) format', 11 | packages = ['nwb'], 12 | install_requires = ['h5py', 'jsonschema'] 13 | ) 14 | 15 | -------------------------------------------------------------------------------- /test_all/make_dirsig.py: -------------------------------------------------------------------------------- 1 | 2 | # This script creates a "signature file" for the contents of all 3 | # files in a directory. The signature file, has a list of all the files 4 | # and a hash code for each. This is used to verify that files generated 5 | # by scripts match those that were originally generated. 6 | 7 | 8 | import sys 9 | import glob 10 | import os, fnmatch 11 | import re 12 | from sys import version_info 13 | from nwb import value_summary as vs 14 | 15 | def error_exit(msg): 16 | if msg: 17 | print(msg) 18 | print ( "Format is") 19 | print ("%s " % sys.argv[0]) 20 | print ("where:") 21 | print (" - a directory containing files, or a single file.") 22 | print (" If a directory is given, a single signature file, named 'dircig.txt'") 23 | print (" is created inside it. If a file is given, the name and hash of the") 24 | print (" file is written to standard output.") 25 | sys.exit(1) 26 | 27 | def remove_sig_somments(contents): 28 | # remove text inside <% ... %> from string contents 29 | # This done to remove text that is likely to be variable across nwb files 30 | # that are the same (such as file_create_date) so it is not used for hash 31 | # comparison 32 | contents = re.sub(b"<%.*?%>", b"", contents) 33 | return contents 34 | 35 | 36 | def get_file_hash(path): 37 | f = open(path, "rb") 38 | contents = f.read() 39 | f.close() 40 | contents = remove_sig_somments(contents) 41 | hash = vs.hashval(contents) 42 | # make sure hash is 6 characters 43 | if len(hash) < 6: 44 | hash = "%s%s" % (hash, hash[1]*(6-len(hash))) # append repeats of second character 45 | return hash 46 | 47 | def process_files(input_dir_or_file): 48 | if os.path.isfile(input_dir_or_file): 49 | hash = get_file_hash(input_dir_or_file) 50 | print ("%s %s" % (hash, input_dir_or_file)) 51 | else: 52 | # input_dir_or_file is a directory, processes files within it 53 | output = [] 54 | output_file_name = "dirsig.txt" 55 | ignore_files = [output_file_name, "log.txt"] 56 | for dirpath, dirnames, filenames in os.walk(input_dir_or_file): 57 | for filename in filenames: 58 | assert dirpath.startswith(input_dir_or_file) 59 | path = os.path.join(dirpath, filename) 60 | if path in [os.path.join(input_dir_or_file, x) for x in ignore_files]: 61 | # don't include signature for this file 62 | continue 63 | hash = get_file_hash(path) 64 | output_path = path[len(input_dir_or_file):].lstrip("/") 65 | output.append("%s %s" % (hash, output_path)) 66 | # print ("dirpath=%s, output_path=%s, filename=%s" % (dirpath, output_path, filename)) 67 | # write output 68 | output_file_path = os.path.join(input_dir_or_file, output_file_name) 69 | f = open(output_file_path, "w") 70 | f.write("\n".join(output)) 71 | f.close() 72 | 73 | if __name__ == '__main__': 74 | if len(sys.argv) != 2: 75 | error_exit("Invalid number of command line arguments: %s" % len(sys.argv)) 76 | input_dir_or_file = sys.argv[1] 77 | if not os.path.exists(input_dir_or_file): 78 | error_exit("Input does not exist: %s" % input_dir_or_file) 79 | process_files(input_dir_or_file) -------------------------------------------------------------------------------- /test_all/set_orig.py: -------------------------------------------------------------------------------- 1 | # script to set the "orig" (original) directory to the "curr" (current) directory 2 | 3 | # Details: 4 | # If orig exists, moves it to orig_bkNN (NN == 01, 02, 03, ...). 5 | # then moves "curr" to "orig". 6 | 7 | import shutil 8 | import os 9 | import glob 10 | import re 11 | 12 | if not os.path.isdir("curr"): 13 | print ("Directory 'curr' does not exist. Cannot set orig to curr. Aborting.") 14 | sys.exit(1) 15 | 16 | if os.path.isdir("orig"): 17 | # orig exists, move it to orig_bkNN 18 | 19 | bk_files=sorted(glob.glob("orig_bk[0-9]*")) 20 | if bk_files: 21 | lastf=bk_files[-1] 22 | match = re.match("orig_bk([0-9]*)", lastf) 23 | if not match: 24 | print("Unable to isolate integer in name: %s" % lastf) 25 | sys.exit(1) 26 | last_num = int(match.group(1)) 27 | next_num =last_num + 1 28 | next_name = "orig_bk%02i" % next_num 29 | # print ("next_name is %s" % next_name) 30 | else: 31 | next_name = "orig_bk01" 32 | print ("Renaming 'orig' => '%s'" % next_name) 33 | os.rename("orig", next_name) 34 | 35 | # now copy 'curr' to 'orig' 36 | print ("Copying 'curr' to 'orig'") 37 | shutil.copytree("curr", "orig") 38 | 39 | print ("all done") 40 | 41 | 42 | 43 | 44 | 45 | -------------------------------------------------------------------------------- /test_all/test_all.cfg: -------------------------------------------------------------------------------- 1 | # configuration file for tests 2 | 3 | # Set below the path to the matlab executable to include matlab tests 4 | # To prevent testing matlab, use an empty path, e.g. 5 | # matlab="" 6 | matlab="/Applications/MATLAB_R2016b.app/bin/matlab" 7 | -------------------------------------------------------------------------------- /test_all/test_all.sh: -------------------------------------------------------------------------------- 1 | # Script to perform all tests 2 | 3 | # Requires existing "orig" directory containing signature file 4 | # ("dirsig.txt"). Builds "curr" directory containing results of 5 | # all scripts and signature file for results. Compares 6 | # curr/dirsig.txt to orig/dirsig.txt 7 | # If these match, all tests pass. 8 | 9 | cwd=`pwd` 10 | 11 | orig_sig="orig/dirsig.txt" 12 | source_data_dir="../examples/source_data_2" 13 | 14 | if [[ ! -e "$orig_sig" ]] ; then 15 | echo "File '$orig/dirsig.txt' does not exist. Cannot run tests." 16 | exit 1 17 | fi 18 | 19 | 20 | if [[ ! -e "$source_data_dir" ]] ; then 21 | echo "" 22 | echo "*** Source data directory is not installed. Do you wish to install it?" 23 | echo "Directory '$source_data_dir' must be installed before running test." 24 | echo "Do you wish to install $source_data_dir (about 1.2GB; 580MB download)?" 25 | echo "Type 1 if Yes. 2 if no." 26 | select yn in "Yes" "No"; do 27 | if [[ "$yn" == "Yes" ]] ; then 28 | cd ../examples/utility_scripts 29 | python install_source_data.py 30 | status=$? 31 | cd $cwd 32 | if [[ "$status" -ne "0" ]] ; then 33 | echo "Tests aborted because $source_data_dir not installed." 34 | exit 1 35 | fi 36 | break ; 37 | else 38 | echo "Tests aborted because $source_data_dir not installed." 39 | exit 1 40 | fi 41 | done 42 | fi 43 | 44 | 45 | ./make_curr.sh 46 | 47 | curr_sig="curr/dirsig.txt" 48 | if [[ ! -e "$curr_sig" ]] ; then 49 | echo "File '$curr_sig' does not exist. Cannot complete tests." 50 | exit 1 51 | fi 52 | 53 | python show_diff.py 54 | 55 | status=$? 56 | 57 | echo 58 | if [[ "$status" -eq "0" ]] ; then 59 | echo "** ALL TESTS PASS **" 60 | else 61 | echo "** ONE OR MORE TESTS FAILED. **" 62 | fi 63 | 64 | 65 | -------------------------------------------------------------------------------- /unittest/0_README.txt: -------------------------------------------------------------------------------- 1 | Directory unittests 2 | 3 | This directory contains the unit tests. To run an individual test, 4 | type: 5 | python 6 | 7 | To run all the test, run bash script: 8 | ./run_tests.sh 9 | 10 | 11 | When run, each test will first output a validation report for 12 | the created NWB file. After that will be a message indicating 13 | whether or not the test PASSES or not. 14 | 15 | Ignore the valdation report for the purposes of determing 16 | if the test passes. 17 | -------------------------------------------------------------------------------- /unittest/run_tests.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | FILES=t_*py 3 | for f in $FILES 4 | do 5 | python $f || >&2 echo "$f FAILED" 6 | done 7 | 8 | -------------------------------------------------------------------------------- /unittest/t_annotation.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | # import nwb 4 | from nwb import nwb_file 5 | from nwb import nwb_utils as utils 6 | 7 | import test_utils as ut 8 | 9 | # test creation of annotation time series 10 | # TESTS AnnotationSeries creation 11 | # TESTS TimeSeries ancestry 12 | 13 | 14 | def test_annotation_series(): 15 | if __file__.startswith("./"): 16 | fname = "s" + __file__[3:-3] + ".nwb" 17 | else: 18 | fname = "s" + __file__[1:-3] + ".nwb" 19 | name = "annot" 20 | # create_annotation_series(fname, name, "acquisition") 21 | create_annotation_series(fname, name, "acquisition/timeseries") 22 | ut.verify_timeseries(fname, name, "acquisition/timeseries", "TimeSeries") 23 | ut.verify_timeseries(fname, name, "acquisition/timeseries", "AnnotationSeries") 24 | # create_annotation_series(fname, name, "stimulus") 25 | create_annotation_series(fname, name, "stimulus/presentation") 26 | ut.verify_timeseries(fname, name, "stimulus/presentation", "TimeSeries") 27 | ut.verify_timeseries(fname, name, "stimulus/presentation", "AnnotationSeries") 28 | 29 | def create_annotation_series(fname, name, target): 30 | settings = {} 31 | settings["file_name"] = fname 32 | settings["identifier"] = utils.create_identifier("annotation example") 33 | settings["mode"] = "w" 34 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 35 | settings["description"] = "Test file with AnnotationSeries" 36 | settings["verbosity"] = "none" 37 | # neurodata = nwb.NWB(**settings) 38 | f = nwb_file.open(**settings) 39 | # annot = neurodata.create_timeseries("AnnotationSeries", name, target) 40 | annot = f.make_group("", name, path="/" + target) 41 | 42 | # annot.set_description("This is an AnnotationSeries with sample data") 43 | annot.set_attr('description', "This is an AnnotationSeries with sample data") 44 | # annot.set_comment("The comment and description fields can store arbitrary human-readable data") 45 | annot.set_attr("comments", "The comment and desscription fields can store arbitrary human-readable data") 46 | # annot.set_source("Observation of Dr. J Doe") 47 | annot.set_attr("source", "Observation of Dr. J Doe") 48 | # 49 | # annot.add_annotation("Rat in bed, beginning sleep 1", 15.0) 50 | # annot.add_annotation("Rat placed in enclosure, start run 1", 933.0) 51 | # annot.add_annotation("Rat taken out of enclosure, end run 1", 1456.0) 52 | # annot.add_annotation("Rat in bed, start sleep 2", 1461.0) 53 | # annot.add_annotation("Rat placed in enclosure, start run 2", 2401.0) 54 | # annot.add_annotation("Rat taken out of enclosure, end run 2", 3210.0) 55 | # annot.add_annotation("Rat in bed, start sleep 3", 3218.0) 56 | # annot.add_annotation("End sleep 3", 4193.0) 57 | # store pretend data 58 | # all time is stored as seconds 59 | andata = [] 60 | andata.append(("Rat in bed, beginning sleep 1", 15.0)) 61 | andata.append(("Rat placed in enclosure, start run 1", 933.0)) 62 | andata.append(("Rat taken out of enclosure, end run 1", 1456.0)) 63 | andata.append(("Rat in bed, start sleep 2", 1461.0)) 64 | andata.append(("Rat placed in enclosure, start run 2", 2401.0)) 65 | andata.append(("Rat taken out of enclosure, end run 2", 3210.0)) 66 | andata.append(("Rat in bed, start sleep 3", 3218.0)) 67 | andata.append(("End sleep 3", 4193.0)) 68 | annotations = [x[0] for x in andata] 69 | times = [x[1] for x in andata] 70 | annot.set_dataset("data",annotations) 71 | annot.set_dataset("timestamps", times) 72 | # 73 | #annot.finalize() 74 | f.close() 75 | 76 | test_annotation_series() 77 | print("%s PASSED" % __file__) 78 | 79 | -------------------------------------------------------------------------------- /unittest/t_append.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import test_utils as ut 3 | # import nwb 4 | from nwb import nwb_file 5 | from nwb import nwb_utils as utils 6 | 7 | # test opening file in append mode 8 | # TESTS modifying existing file 9 | # TESTS creation of modification_time 10 | # TESTS addition of TimeSeries to existing file 11 | # TESTS preservation of TimeSeries when file modified 12 | 13 | def test_append(): 14 | if __file__.startswith("./"): 15 | fname = "s" + __file__[3:-3] + ".nwb" 16 | else: 17 | fname = "s" + __file__[1:-3] + ".nwb" 18 | name1 = "annot1" 19 | name2 = "annot2" 20 | # create_annotation_series(fname, name1, "acquisition", True) 21 | create_annotation_series(fname, name1, "acquisition/timeseries", True) 22 | # create_annotation_series(fname, name2, "acquisition", False) 23 | create_annotation_series(fname, name2, "acquisition/timeseries", False) 24 | ut.verify_timeseries(fname, name1, "acquisition/timeseries", "TimeSeries") 25 | ut.verify_timeseries(fname, name1, "acquisition/timeseries", "AnnotationSeries") 26 | ut.verify_timeseries(fname, name2, "acquisition/timeseries", "TimeSeries") 27 | ut.verify_timeseries(fname, name2, "acquisition/timeseries", "AnnotationSeries") 28 | # ut.verify_attribute_present(fname, "file_create_date", "modification_time") 29 | 30 | 31 | def create_annotation_series(fname, name, target, newfile): 32 | settings = {} 33 | settings["file_name"] = fname 34 | settings["verbosity"] = "none" 35 | if newfile: 36 | settings["identifier"] = utils.create_identifier("append example") 37 | settings["mode"] = "w" 38 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 39 | settings["description"] = "Test append file" 40 | else: 41 | settings["mode"] = "r+" 42 | f = nwb_file.open(**settings) 43 | # 44 | # annot = neurodata.create_timeseries("AnnotationSeries", name, target) 45 | annot = f.make_group("", name, path="/" + target) 46 | # annot.set_description("This is an AnnotationSeries '%s' with sample data" % name) 47 | # annot.set_comment("The comment and description fields can store arbitrary human-readable data") 48 | # annot.set_source("Observation of Dr. J Doe") 49 | annot.set_attr("description", "This is an AnnotationSeries '%s' with sample data" % name) 50 | annot.set_attr("comments", "The comment and description fields can store arbitrary human-readable data") 51 | annot.set_attr("source", "Observation of Dr. J Doe") 52 | 53 | # 54 | # annot.add_annotation("Rat in bed, beginning sleep 1", 15.0) 55 | # annot.add_annotation("Rat placed in enclosure, start run 1", 933.0) 56 | # annot.add_annotation("Rat taken out of enclosure, end run 1", 1456.0) 57 | # annot.add_annotation("Rat in bed, start sleep 2", 1461.0) 58 | # annot.add_annotation("Rat placed in enclosure, start run 2", 2401.0) 59 | # annot.add_annotation("Rat taken out of enclosure, end run 2", 3210.0) 60 | # annot.add_annotation("Rat in bed, start sleep 3", 3218.0) 61 | # annot.add_annotation("End sleep 3", 4193.0) 62 | # 63 | 64 | andata = [] 65 | andata.append(("Rat in bed, beginning sleep 1", 15.0)) 66 | andata.append(("Rat placed in enclosure, start run 1", 933.0)) 67 | andata.append(("Rat taken out of enclosure, end run 1", 1456.0)) 68 | andata.append(("Rat in bed, start sleep 2", 1461.0)) 69 | andata.append(("Rat placed in enclosure, start run 2", 2401.0)) 70 | andata.append(("Rat taken out of enclosure, end run 2", 3210.0)) 71 | andata.append(("Rat in bed, start sleep 3", 3218.0)) 72 | andata.append(("End sleep 3", 4193.0)) 73 | annotations = [x[0] for x in andata] 74 | times = [x[1] for x in andata] 75 | annot.set_dataset("data",annotations) 76 | annot.set_dataset("timestamps", times) 77 | 78 | # annot.finalize() 79 | # neurodata.close() 80 | f.close() 81 | 82 | test_append() 83 | print("%s PASSED" % __file__) 84 | 85 | -------------------------------------------------------------------------------- /unittest/t_epoch_tag.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | # import nwb 4 | from nwb import nwb_file 5 | from nwb import nwb_utils as utils 6 | import test_utils as ut 7 | 8 | # create two epochs, add different subset of tags to each 9 | # verify main epoch folder has tag attribute that contains 10 | # exactly the unique tags of each epoch and that each 11 | # epoch contains the assigned tags 12 | 13 | if __file__.startswith("./"): 14 | fname = "s" + __file__[3:-3] + ".nwb" 15 | else: 16 | fname = "s" + __file__[1:-3] + ".nwb" 17 | # borg = ut.create_new_file(fname, "Epoch tags") 18 | 19 | f = nwb_file.open(fname, 20 | start_time="2008-09-15T15:53:00-08:00", 21 | mode="w", 22 | identifier=utils.create_identifier("Epoch tags"), 23 | description="softlink test", 24 | verbosity="none") 25 | 26 | tags = ["tag-a", "tag-b", "tag-c"] 27 | 28 | # epoch1 = borg.create_epoch("epoch-1", 0, 3); 29 | 30 | epoch1 = f.make_group("", "epoch-1") 31 | epoch1.set_dataset("start_time", 0) 32 | epoch1.set_dataset("stop_time", 3) 33 | 34 | # for i in range(len(tags)-1): 35 | # epoch1.add_tag(tags[i+1]) 36 | epoch1.set_dataset("tags", tags[1:]) 37 | 38 | # epoch2 = borg.create_epoch("epoch-2", 1, 4); 39 | epoch2 = f.make_group("", "epoch-2") 40 | epoch2.set_dataset("start_time", 1) 41 | epoch2.set_dataset("stop_time", 4) 42 | 43 | # for i in range(len(tags)-1): 44 | # epoch2.add_tag(tags[i]) 45 | epoch2.set_dataset("tags", tags[0:-1]) 46 | 47 | f.close() 48 | 49 | # this test modified because tags are stored as dataset rather than attribute 50 | # tags = ut.verify_attribute_present(fname, "epochs/epoch-1", "tags"); 51 | tags = ut.verify_present(fname, "epochs/epoch-1", "tags"); 52 | for i in range(len(tags)-1): 53 | if tags[i+1] not in tags: 54 | ut.error("Verifying epoch tag content", "All tags not present") 55 | 56 | # tags = ut.verify_attribute_present(fname, "epochs/epoch-2", "tags"); 57 | tags = ut.verify_present(fname, "epochs/epoch-2", "tags"); 58 | for i in range(len(tags)-1): 59 | if tags[i] not in tags: 60 | ut.error("Verifying epoch tag content", "All tags not present") 61 | 62 | tags = ut.verify_attribute_present(fname, "epochs", "tags"); 63 | for i in range(len(tags)): 64 | if tags[i] not in tags: 65 | ut.error("Verifying epoch tag content", "All tags not present") 66 | 67 | 68 | print("%s PASSED" % __file__) 69 | 70 | -------------------------------------------------------------------------------- /unittest/t_general_opto.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import nwb 3 | # from nwb.nwbco import * 4 | import test_utils as ut 5 | 6 | from nwb import nwb_file 7 | from nwb import nwb_utils as utils 8 | 9 | # TESTS fields stored in general/optogenetics 10 | 11 | def test_field(fname, name, subdir): 12 | val = ut.verify_present(fname, "general/optogenetics/"+subdir+"/", name.lower()) 13 | if not ut.strcmp(val, name): 14 | ut.error("Checking metadata", "field value incorrect") 15 | 16 | def test_general_optogen(): 17 | if __file__.startswith("./"): 18 | fname = "s" + __file__[3:-3] + ".nwb" 19 | else: 20 | fname = "s" + __file__[1:-3] + ".nwb" 21 | create_general_optogen(fname) 22 | # 23 | val = ut.verify_present(fname, "general/optogenetics/", "optogen_custom") 24 | if not ut.strcmp(val, "OPTOGEN_CUSTOM"): 25 | ut.error("Checking custom", "Field value incorrect") 26 | # 27 | 28 | test_field(fname, "DESCRIPTION", "p1") 29 | #test_field(fname, "DESCRIPTIONx", "p1") 30 | #test_field(fname, "DESCRIPTION", "p1x") 31 | test_field(fname, "DEVICE", "p1") 32 | # test_field(fname, "LAMBDA", "p1") 33 | test_field(fname, "EXCITATION_LAMBDA", "p1") 34 | test_field(fname, "LOCATION", "p1") 35 | val = ut.verify_present(fname, "general/optogenetics/p1/", "optogen_site_custom") 36 | if not ut.strcmp(val, "OPTOGEN_SITE_CUSTOM"): 37 | ut.error("Checking metadata", "field value incorrect") 38 | 39 | 40 | def create_general_optogen(fname): 41 | settings = {} 42 | settings["start_time"] = "2008-09-15T15:53:00-08:00" 43 | settings["file_name"] = fname 44 | settings["identifier"] = utils.create_identifier("metadata optogenetic test") 45 | settings["mode"] = "w" 46 | settings["description"] = "test elements in /general/optogentics" 47 | settings["verbosity"] = "none" 48 | f = nwb_file.open(**settings) 49 | 50 | 51 | # neurodata.set_metadata(OPTOGEN_CUSTOM("optogen_custom"), "OPTOGEN_CUSTOM") 52 | # # 53 | # neurodata.set_metadata(OPTOGEN_SITE_DESCRIPTION("p1"), "DESCRIPTION") 54 | # neurodata.set_metadata(OPTOGEN_SITE_DEVICE("p1"), "DEVICE") 55 | # neurodata.set_metadata(OPTOGEN_SITE_LAMBDA("p1"), "LAMBDA") 56 | # neurodata.set_metadata(OPTOGEN_SITE_LOCATION("p1"), "LOCATION") 57 | # neurodata.set_metadata(OPTOGEN_SITE_CUSTOM("p1", "optogen_site_custom"), "OPTOGEN_SITE_CUSTOM") 58 | # 59 | 60 | g = f.make_group("optogenetics") 61 | g.set_custom_dataset("optogen_custom", "OPTOGEN_CUSTOM") 62 | 63 | p1 = g.make_group("", "p1") 64 | p1.set_dataset("description","DESCRIPTION") 65 | p1.set_dataset("device", "DEVICE") 66 | p1.set_dataset("excitation_lambda","EXCITATION_LAMBDA") 67 | p1.set_dataset("location", "LOCATION") 68 | p1.set_custom_dataset("optogen_site_custom", "OPTOGEN_SITE_CUSTOM") 69 | 70 | # neurodata.close() 71 | f.close() 72 | 73 | test_general_optogen() 74 | print("%s PASSED" % __file__) 75 | 76 | -------------------------------------------------------------------------------- /unittest/t_general_species.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | # import nwb 3 | # from nwb.nwbco import * 4 | import test_utils as ut 5 | 6 | from nwb import nwb_file 7 | from nwb import nwb_utils as utils 8 | 9 | # TESTS fields stored in general/subject 10 | 11 | def test_field(fname, name): 12 | val = ut.verify_present(fname, "general/subject/", name.lower()) 13 | if not ut.strcmp(val, name): 14 | ut.error("Checking metadata", "field value incorrect") 15 | 16 | def test_general_subject(): 17 | if __file__.startswith("./"): 18 | fname = "s" + __file__[3:-3] + ".nwb" 19 | else: 20 | fname = "s" + __file__[1:-3] + ".nwb" 21 | create_general_subject(fname) 22 | val = ut.verify_present(fname, "general/subject/", "description") 23 | if not ut.strcmp(val, "SUBJECT"): 24 | ut.error("Checking metadata", "field value incorrect") 25 | test_field(fname, "SUBJECT_ID") 26 | test_field(fname, "SPECIES") 27 | test_field(fname, "GENOTYPE") 28 | test_field(fname, "SEX") 29 | test_field(fname, "AGE") 30 | test_field(fname, "WEIGHT") 31 | 32 | 33 | def create_general_subject(fname): 34 | settings = {} 35 | settings["file_name"] = fname 36 | settings["start_time"] = "2008-09-15T15:53:00-08:00" 37 | settings["identifier"] = utils.create_identifier("general top test") 38 | settings["mode"] = "w" 39 | settings["description"] = "test elements in /general/subject" 40 | settings["verbosity"] = "none" 41 | f = nwb_file.open(**settings) 42 | 43 | 44 | # 45 | # neurodata.set_metadata(SUBJECT, "SUBJECT") 46 | # neurodata.set_metadata(SUBJECT_ID, "SUBJECT_ID") 47 | # neurodata.set_metadata(SPECIES, "SPECIES") 48 | # neurodata.set_metadata(GENOTYPE, "GENOTYPE") 49 | # neurodata.set_metadata(SEX, "SEX") 50 | # neurodata.set_metadata(AGE, "AGE") 51 | # neurodata.set_metadata(WEIGHT, "WEIGHT") 52 | # 53 | 54 | g = f.make_group("subject") 55 | g.set_dataset("description", "SUBJECT") 56 | g.set_dataset("subject_id", "SUBJECT_ID") 57 | g.set_dataset("species", "SPECIES") 58 | g.set_dataset("genotype", "GENOTYPE") 59 | g.set_dataset("sex", "SEX") 60 | g.set_dataset("age", "AGE") 61 | g.set_dataset("weight", "WEIGHT") 62 | 63 | # neurodata.close() 64 | f.close() 65 | 66 | test_general_subject() 67 | print("%s PASSED" % __file__) 68 | 69 | -------------------------------------------------------------------------------- /unittest/t_if_add_ts.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import test_utils as ut 3 | import numpy as np 4 | # import nwb 5 | 6 | from nwb import nwb_file 7 | from nwb import nwb_utils as utils 8 | 9 | 10 | # test opening file in append mode 11 | # TESTS creating a module 12 | # TESTS creating an interface 13 | # TESTS adding a timeseries to an interface 14 | 15 | def test_file(): 16 | if __file__.startswith("./"): 17 | fname = "s" + __file__[3:-3] + ".nwb" 18 | else: 19 | fname = "s" + __file__[1:-3] + ".nwb" 20 | create_iface_series(fname, True) 21 | name1 = "Ones" 22 | ut.verify_timeseries(fname, name1, "processing/test module/BehavioralEvents", "TimeSeries") 23 | 24 | 25 | def create_iface_series(fname, newfile): 26 | settings = {} 27 | settings["file_name"] = fname 28 | settings["verbosity"] = "none" 29 | if newfile: 30 | settings["identifier"] = utils.create_identifier("interface timeseries example") 31 | settings["mode"] = "w" 32 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 33 | settings["description"] = "Test interface timeseries file" 34 | else: 35 | settings["mode"] = "r+" 36 | f = nwb_file.open(**settings) 37 | # 38 | # mod = neurodata.create_module("test module") 39 | # iface = mod.create_interface("BehavioralEvents") 40 | # ts = neurodata.create_timeseries("TimeSeries", "Ones") 41 | # ts.set_data(np.ones(10), unit="Event", conversion=1.0, resolution=float('nan')) 42 | # ts.set_value("num_samples", 10) 43 | # ts.set_time(np.arange(10)) 44 | # iface.add_timeseries(ts) 45 | # iface.finalize() 46 | # mod.finalize() 47 | 48 | 49 | mod = f.make_group("", "test module") 50 | iface = mod.make_group("BehavioralEvents") 51 | ts = iface.make_group("", "Ones") 52 | ts.set_dataset("data", np.ones(10), attrs={'unit':"Event", 53 | "conversion":1.0, "resolution": float('nan')}) 54 | ts.set_dataset("num_samples", 10) 55 | ts.set_dataset("timestamps",np.arange(10)) 56 | 57 | # 58 | # neurodata.close() 59 | f.close() 60 | 61 | test_file() 62 | print("%s PASSED" % __file__) 63 | 64 | -------------------------------------------------------------------------------- /unittest/t_modification_time.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import h5py 3 | import sys 4 | # import nwb 5 | import test_utils as ut 6 | import time 7 | 8 | from nwb import nwb_file 9 | from nwb import nwb_utils as utils 10 | 11 | # creates file and modifies it multiple times 12 | 13 | if __file__.startswith("./"): 14 | fname = "s" + __file__[3:-3] + ".nwb" 15 | else: 16 | fname = "s" + __file__[1:-3] + ".nwb" 17 | 18 | settings = {} 19 | settings["file_name"] = fname 20 | settings["identifier"] = utils.create_identifier("Modification example") 21 | settings["mode"] = "w" 22 | settings["description"] = "Modified empty file" 23 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 24 | settings["verbosity"] = "none" 25 | 26 | f = nwb_file.open(**settings) 27 | f.close() 28 | 29 | #time.sleep(1) 30 | settings = {} 31 | settings["file_name"] = fname 32 | settings["mode"] = "r+" 33 | settings["verbosity"] = "none" 34 | f = nwb_file.open(**settings) 35 | # need to actually change the file for SLAPI to update file_create_date 36 | f.set_dataset("species", "SPECIES") 37 | f.close() 38 | 39 | #time.sleep(1) 40 | settings = {} 41 | settings["file_name"] = fname 42 | settings["mode"] = "r+" 43 | settings["verbosity"] = "none" 44 | f = nwb_file.open(**settings) 45 | # need to actually change the file for SLAPI to update file_create_date 46 | f.set_dataset("genotype", "GENOTYPE") 47 | f.close() 48 | 49 | f = h5py.File(fname) 50 | dates = f["file_create_date"] 51 | if len(dates) != 3: 52 | ut.error(__file__, "Expected 3 entries in file_create_date; found %d" % len(dates)) 53 | 54 | print("%s PASSED" % __file__) 55 | 56 | -------------------------------------------------------------------------------- /unittest/t_no_data.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | # import nwb 4 | import test_utils as ut 5 | 6 | from nwb import nwb_file 7 | from nwb import nwb_utils as utils 8 | 9 | # creates time series without 'data' field 10 | # TESTS TimeSeries.ignore_data() 11 | 12 | def test_nodata_series(): 13 | if __file__.startswith("./"): 14 | fname = "s" + __file__[3:-3] + ".nwb" 15 | else: 16 | fname = "s" + __file__[1:-3] + ".nwb" 17 | name = "nodata" 18 | # create_nodata_series(fname, name, "acquisition") 19 | create_nodata_series(fname, name, "/acquisition/timeseries") 20 | ut.verify_timeseries(fname, name, "acquisition/timeseries", "TimeSeries") 21 | ut.verify_absent(fname, "acquisition/timeseries/"+name, "data") 22 | 23 | def create_nodata_series(fname, name, target): 24 | settings = {} 25 | settings["file_name"] = fname 26 | settings["identifier"] = utils.create_identifier("nodata example") 27 | settings["mode"] = "w" 28 | settings["description"] = "time series no data test" 29 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 30 | settings["verbosity"] = "none" 31 | f = nwb_file.open(**settings) 32 | 33 | 34 | # 35 | # nodata = neurodata.create_timeseries("TimeSeries", name, target) 36 | # nodata.ignore_data() 37 | # nodata.set_time([0]) 38 | 39 | nodata = f.make_group("", name, path=target) 40 | nodata.set_dataset("timestamps", [0]) 41 | # 42 | # nodata.finalize() 43 | # neurodata.close() 44 | f.close() 45 | 46 | test_nodata_series() 47 | print("%s PASSED" % __file__) 48 | 49 | -------------------------------------------------------------------------------- /unittest/t_no_time.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | # import nwb 4 | import test_utils as ut 5 | 6 | from nwb import nwb_file 7 | from nwb import nwb_utils as utils 8 | 9 | # creates time series without 'timestamps' or 'starting_time' fields 10 | # TESTS TimeSeries.ignore_time() 11 | # TESTS timeseries placement in acquisition, stimulus, templates 12 | 13 | def test_notime_series(): 14 | if __file__.startswith("./"): 15 | fname = "s" + __file__[3:-3] + ".nwb" 16 | else: 17 | fname = "s" + __file__[1:-3] + ".nwb" 18 | name = "notime" 19 | # create_notime_series(fname, name, "acquisition") 20 | create_notime_series(fname, name, "/acquisition/timeseries") 21 | ut.verify_timeseries(fname, name, "acquisition/timeseries", "TimeSeries") 22 | ut.verify_absent(fname, "acquisition/timeseries/"+name, "timestamps") 23 | ut.verify_absent(fname, "acquisition/timeseries/"+name, "starting_time") 24 | 25 | # create_notime_series(fname, name, "stimulus") 26 | create_notime_series(fname, name, "/stimulus/presentation") 27 | ut.verify_timeseries(fname, name, "stimulus/presentation", "TimeSeries") 28 | # create_notime_series(fname, name, "template") 29 | create_notime_series(fname, name, "/stimulus/templates") 30 | ut.verify_timeseries(fname, name, "stimulus/templates", "TimeSeries") 31 | 32 | def create_notime_series(fname, name, target): 33 | settings = {} 34 | settings["file_name"] = fname 35 | settings["identifier"] = utils.create_identifier("notime example") 36 | settings["mode"] = "w" 37 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 38 | settings["description"] = "Test no time" 39 | settings["verbosity"] = "none" 40 | f = nwb_file.open(**settings) 41 | 42 | 43 | # 44 | # notime = neurodata.create_timeseries("TimeSeries", name, target) 45 | # notime.ignore_time() 46 | # notime.set_data([0], unit="n/a", conversion=1, resolution=1) 47 | 48 | notime = f.make_group("", name, path=target) 49 | # following used for testing more missing_fields 50 | # notime = f.make_group("", name, path=target) 51 | notime.set_dataset("data", [0.0], attrs={"unit":"n/a", 52 | "conversion":1.0, "resolution":1.0}) 53 | 54 | # 55 | # notime.finalize() 56 | # neurodata.close() 57 | f.close() 58 | 59 | test_notime_series() 60 | print("%s PASSED" % __file__) 61 | 62 | -------------------------------------------------------------------------------- /unittest/t_ref_image.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | # import nwb 3 | import test_utils as ut 4 | 5 | from nwb import nwb_file 6 | from nwb import nwb_utils as utils 7 | 8 | 9 | # TESTS storage of reference image 10 | 11 | def test_refimage_series(): 12 | if __file__.startswith("./"): 13 | fname = "s" + __file__[3:-3] + ".nwb" 14 | else: 15 | fname = "s" + __file__[1:-3] + ".nwb" 16 | name = "refimage" 17 | create_refimage(fname, name) 18 | val = ut.verify_present(fname, "acquisition/images/", name) 19 | #if len(val) != 6: 20 | if len(val) != 5: 21 | ut.error("Checking ref image contents", "wrong dimension") 22 | val = ut.verify_attribute_present(fname, "acquisition/images/"+name, "format") 23 | if not ut.strcmp(val, "raw"): 24 | ut.error("Checking ref image format", "Wrong value") 25 | val = ut.verify_attribute_present(fname, "acquisition/images/"+name, "description") 26 | if not ut.strcmp(val, "test"): 27 | ut.error("Checking ref image description", "Wrong value") 28 | 29 | def create_refimage(fname, name): 30 | settings = {} 31 | settings["file_name"] = fname 32 | settings["start_time"] = "2008-09-15T15:53:00-08:00" 33 | settings["identifier"] = utils.create_identifier("reference image test") 34 | settings["mode"] = "w" 35 | settings["description"] = "reference image test" 36 | settings["verbosity"] = "none" 37 | f = nwb_file.open(**settings) 38 | 39 | # neurodata.create_reference_image([1,2,3,4,5], name, "raw", "test") 40 | f.set_dataset("", [1,2,3,4,5], dtype="uint8", name=name, attrs={ 41 | "description": "test", "format":"raw"}) 42 | 43 | # neurodata.close() 44 | f.close() 45 | 46 | test_refimage_series() 47 | print("%s PASSED" % __file__) 48 | 49 | -------------------------------------------------------------------------------- /unittest/t_softlink.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import sys 3 | # import nwb 4 | import test_utils as ut 5 | 6 | from nwb import nwb_file 7 | from nwb import nwb_utils as utils 8 | 9 | # creates time series without 'data' field 10 | # TESTS softlink of TimeSeries.data 11 | 12 | def test_softlink(): 13 | if __file__.startswith("./"): 14 | fname1 = "s" + __file__[3:-3] + "1" + ".nwb" 15 | fname2 = "s" + __file__[3:-3] + "2" + ".nwb" 16 | else: 17 | fname1 = "s" + __file__[1:-3] + "1" + ".nwb" 18 | fname2 = "s" + __file__[1:-3] + "2" + ".nwb" 19 | name1 = "softlink_source" 20 | name2 = "softlink_reader" 21 | # create_softlink_source(fname1, name1, "acquisition") 22 | # create_softlink_reader(fname2, name2, fname1, name1, "acquisition") 23 | create_softlink_source(fname1, name1, "/acquisition/timeseries") 24 | create_softlink_reader(fname2, name2, fname1, name1, "/acquisition/timeseries") 25 | # 26 | ut.verify_timeseries(fname1, name1, "acquisition/timeseries", "TimeSeries") 27 | ut.verify_timeseries(fname2, name2, "acquisition/timeseries", "TimeSeries") 28 | ## 29 | val = ut.verify_present(fname2, "acquisition/timeseries/"+name2, "data") 30 | 31 | def create_softlink_reader(fname, name, src_fname, src_name, target): 32 | settings = {} 33 | settings["file_name"] = fname 34 | settings["start_time"] = "2008-09-15T15:53:00-08:00" 35 | settings["identifier"] = utils.create_identifier("softlink reader") 36 | settings["mode"] = "w" 37 | settings["description"] = "softlink test" 38 | settings["verbosity"] = "none" 39 | f = nwb_file.open(**settings) 40 | 41 | # source = neurodata.create_timeseries("TimeSeries", name, target) 42 | # source.set_data_as_remote_link(src_fname, "acquisition/timeseries/"+src_name+"/data") 43 | # source.set_time([345]) 44 | # source.finalize() 45 | # neurodata.close() 46 | 47 | source = f.make_group("", name, path=target) 48 | # source.set_data_as_remote_link(src_fname, "acquisition/timeseries/"+src_name+"/data") 49 | extlink = "extlink:%s,%s" % (src_fname, "acquisition/timeseries/"+src_name+"/data") 50 | source.set_dataset("data", extlink) 51 | source.set_dataset("timestamps", [345]) 52 | # source.finalize() 53 | # neurodata.close() 54 | f.close() 55 | 56 | def create_softlink_source(fname, name, target): 57 | settings = {} 58 | settings["file_name"] = fname 59 | settings["identifier"] = utils.create_identifier("softlink source") 60 | settings["mode"] = "w" 61 | settings["description"] = "time series no data test" 62 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 63 | settings["verbosity"] = "none" 64 | f = nwb_file.open(**settings) 65 | # source = neurodata.create_timeseries("TimeSeries", name, target) 66 | source = f.make_group("", name, path=target) 67 | # source.set_data([234], unit="parsec", conversion=1.0, resolution=1e-3) 68 | source.set_dataset("data", [234.0], attrs={"unit":"parsec", 69 | "conversion":1.0, "resolution":1e-3}) 70 | # source.set_time([123]) 71 | source.set_dataset("timestamps", [123.0]) 72 | # source.finalize() 73 | # neurodata.close() 74 | f.close() 75 | 76 | test_softlink() 77 | print("%s PASSED" % __file__) 78 | 79 | -------------------------------------------------------------------------------- /unittest/t_starting_time.py: -------------------------------------------------------------------------------- 1 | 2 | #!/usr/bin/python 3 | # import nwb 4 | import test_utils as ut 5 | 6 | from nwb import nwb_file 7 | from nwb import nwb_utils as utils 8 | 9 | # TESTS use of TimeSeries.starting_time 10 | 11 | def test_nodata_series(): 12 | if __file__.startswith("./"): 13 | fname = "s" + __file__[3:-3] + ".nwb" 14 | else: 15 | fname = "s" + __file__[1:-3] + ".nwb" 16 | name = "starting_time" 17 | # create_startingtime_series(fname, name, "acquisition") 18 | create_startingtime_series(fname, name, "/acquisition/timeseries") 19 | ut.verify_timeseries(fname, name, "acquisition/timeseries", "TimeSeries") 20 | ut.verify_absent(fname, "acquisition/timeseries/"+name, "timestamps") 21 | val = ut.verify_present(fname, "acquisition/timeseries/"+name, "starting_time") 22 | if val != 0.125: 23 | ut.error("Checking start time", "Incorrect value") 24 | val = ut.verify_attribute_present(fname, "acquisition/timeseries/starting_time/"+name, "rate") 25 | if val != 2: 26 | ut.error("Checking rate", "Incorrect value") 27 | 28 | def create_startingtime_series(fname, name, target): 29 | settings = {} 30 | settings["file_name"] = fname 31 | settings["identifier"] = utils.create_identifier("starting time test") 32 | settings["mode"] = "w" 33 | settings["description"] = "time series starting time test" 34 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 35 | settings["verbosity"] = "none" 36 | f = nwb_file.open(**settings) 37 | 38 | # 39 | # stime = neurodata.create_timeseries("TimeSeries", name, target) 40 | # stime.set_data([0, 1, 2, 3], unit="n/a", conversion=1, resolution=1) 41 | # stime.set_value("num_samples", 4) 42 | # stime.set_time_by_rate(0.125, 2) 43 | # 44 | 45 | stime = f.make_group("", name, path=target) 46 | stime.set_dataset("data", [0.0, 1.0, 2.0, 3.0], attrs={"unit": "n/a", 47 | "conversion":1.0, "resolution": 1.0}) 48 | stime.set_dataset("num_samples", 4) 49 | 50 | # stime.set_time_by_rate(0.125, 2) 51 | stime.set_dataset("starting_time", 0.125, attrs={ "rate":2.0, "unit":"Seconds"}) 52 | # stime.finalize() 53 | # neurodata.close() 54 | f.close() 55 | 56 | test_nodata_series() 57 | print("%s PASSED" % __file__) 58 | 59 | -------------------------------------------------------------------------------- /unittest/t_top_datasets.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | # import nwb 3 | import test_utils as ut 4 | 5 | from nwb import nwb_file 6 | from nwb import nwb_utils as utils 7 | 8 | # TESTS top-level datasets 9 | 10 | def test_refimage_series(): 11 | if __file__.startswith("./"): 12 | fname = "s" + __file__[3:-3] + ".nwb" 13 | else: 14 | fname = "s" + __file__[1:-3] + ".nwb" 15 | name = "refimage" 16 | create_refimage(fname, name) 17 | val = ut.verify_present(fname, "/", "identifier") 18 | if not ut.strcmp(val, "vwx"): 19 | ut.error("Checking file idenfier", "wrong contents") 20 | val = ut.verify_present(fname, "/", "file_create_date") 21 | val = ut.verify_present(fname, "/", "session_start_time") 22 | if not ut.strcmp(val, "xyz"): 23 | ut.error("Checking session start time", "wrong contents") 24 | val = ut.verify_present(fname, "/", "session_description") 25 | if not ut.strcmp(val, "wxy"): 26 | ut.error("Checking session start time", "wrong contents") 27 | 28 | def create_refimage(fname, name): 29 | settings = {} 30 | settings["file_name"] = fname 31 | settings["identifier"] = "vwx" 32 | settings["mode"] = "w" 33 | settings["description"] = "wxy" 34 | settings["start_time"] = "xyz" 35 | settings["verbosity"] = "none" 36 | f = nwb_file.open(**settings) 37 | # neurodata.close() 38 | f.close() 39 | 40 | test_refimage_series() 41 | print("%s PASSED" % __file__) 42 | 43 | -------------------------------------------------------------------------------- /unittest/t_unittimes.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import h5py 3 | import sys 4 | # import nwb 5 | import test_utils as ut 6 | 7 | from nwb import nwb_file 8 | from nwb import nwb_utils as utils 9 | 10 | # TESTS creation of UnitTimes interface and data stored within 11 | 12 | 13 | def test_unit_times(): 14 | if __file__.startswith("./"): 15 | fname = "s" + __file__[3:-3] + ".nwb" 16 | else: 17 | fname = "s" + __file__[1:-3] + ".nwb" 18 | # create the file we're going to use 19 | ndata = create_empty_file(fname) 20 | # create a module to store processed data 21 | # mod = ndata.create_module("my spike times") 22 | mod = ndata.make_group("", "my spike times") 23 | # ad a unit times interface to the module 24 | # iface = mod.create_interface("UnitTimes") 25 | iface = mod.make_group("UnitTimes") 26 | # make some data to store 27 | spikes = create_spikes() 28 | # for i in range(len(spikes)): 29 | # iface.add_unit(unit_name = "unit-%d" % i, 30 | # unit_times = spikes[i], 31 | # description = "", 32 | # source = "Data spike-sorted by B. Bunny") 33 | 34 | for i in range(len(spikes)): 35 | unit_name = "unit-%d" % i 36 | ug = iface.make_group("", unit_name) 37 | ug.set_dataset("times", spikes[i]) 38 | ug.set_dataset("unit_description", "") 39 | ug.set_dataset("source", "Data spike-sorted by B. Bunny") 40 | 41 | 42 | # clean up and close objects 43 | # iface.finalize() 44 | # mod.finalize() 45 | ndata.close() 46 | 47 | # test random sample to make sure data was stored correctly 48 | h5 = h5py.File(fname) 49 | times = h5["processing/my spike times/UnitTimes/unit-0/times"].value 50 | assert len(times) == len(spikes[0]), "Spike count for unit-0 wrong" 51 | assert abs(times[1] - spikes[0][1]) < 0.001, "Wrong time found in file" 52 | h5.close() 53 | 54 | 55 | def create_spikes(): 56 | spikes = [] 57 | spikes.append([1.3, 1.4, 1.9, 2.1, 2.2, 2.3]) 58 | spikes.append([2.2, 3.0]) 59 | spikes.append([0.3, 0.4, 1.0, 1.1, 1.45, 1.8, 1.81, 2.2]) 60 | return spikes 61 | 62 | def create_empty_file(fname): 63 | settings = {} 64 | settings["file_name"] = fname 65 | settings["identifier"] = utils.create_identifier("UnitTimes example") 66 | settings["mode"] = "w" 67 | settings["start_time"] = "Sat Jul 04 2015 3:14:16" 68 | settings["description"] = "Test file with spike times in processing module" 69 | settings["verbosity"] = "none" 70 | f = nwb_file.open(**settings) 71 | return f 72 | 73 | test_unit_times() 74 | print("%s PASSED" % __file__) 75 | 76 | --------------------------------------------------------------------------------