├── .github └── workflows │ └── black.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CITATION.cff ├── LICENSE.txt ├── README.md ├── images ├── demo.gif └── py4DSTEM_logo.png ├── py4DGUI-keymap.html ├── pyproject.toml └── src └── py4D_browser ├── __init__.py ├── dialogs.py ├── empad2_reader.py ├── help_menu.py ├── logo.png ├── main_window.py ├── menu_actions.py ├── py4DGUI-keymap.png ├── runGUI.py ├── scalebar.py ├── update_views.py └── utils.py /.github/workflows/black.yml: -------------------------------------------------------------------------------- 1 | name: Check code style 2 | 3 | on: 4 | push: 5 | branches: [ "dev" ] 6 | pull_request: 7 | branches: [ "dev" ] 8 | 9 | jobs: 10 | lint: 11 | runs-on: ubuntu-latest 12 | steps: 13 | - uses: actions/checkout@v3 14 | - uses: psf/black@stable 15 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | .project 3 | .pydevproject 4 | *.swp 5 | *.ipynb_checkpoints* 6 | pyrightconfig.json 7 | 8 | # Folders # 9 | .idea/ 10 | __pycache__/ 11 | *.egg-info/ 12 | build/ 13 | dist/ 14 | #py4DSTEM/sample_code/ 15 | py4DSTEM/test/testdata/ 16 | sample_code/data/*h5 17 | sample_code/data/*dm3 18 | py4DSTEM/test/unit_test_data/ 19 | .vscode 20 | # Data Specific # 21 | ################# 22 | #*.png 23 | #*.gif 24 | *.emd 25 | *.emf 26 | *.dm3 27 | *.dm4 28 | *.tiff 29 | *.tif 30 | *.jpg 31 | *.avi 32 | *.mp4 33 | *.emd 34 | *.pdf 35 | *.bin 36 | *.mat 37 | *.doc 38 | *.docx 39 | *.xlsx 40 | *.asv 41 | *.eps 42 | *.fig 43 | *.ai 44 | *.avi 45 | *.m~ 46 | *.db 47 | *.eps 48 | *.asv 49 | *.svg 50 | *.emf 51 | 52 | # Compiled source # 53 | ################### 54 | *.com 55 | *.class 56 | *.dll 57 | *.exe 58 | *.o 59 | *.so 60 | *.mex* 61 | 62 | # Packages # 63 | ############ 64 | # it's better to unpack these files and commit the raw source 65 | # git has its own built in compression methods 66 | *.7z 67 | *.dmg 68 | *.gz 69 | *.iso 70 | *.jar 71 | *.rar 72 | *.tar 73 | *.zip 74 | 75 | # Logs and databases # 76 | ###################### 77 | *.log 78 | *.sql 79 | *.sqlite 80 | 81 | # OS generated files # 82 | ###################### 83 | .DS_Store 84 | .DS_Store? 85 | ._* 86 | .Spotlight-V100 87 | .Trashes 88 | ehthumbs.db 89 | Thumbs.db 90 | Untitled.ipynb 91 | -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- 1 | # See https://pre-commit.com for more information 2 | # See https://pre-commit.com/hooks.html for more hooks 3 | repos: 4 | - repo: https://github.com/pre-commit/pre-commit-hooks 5 | rev: v3.2.0 6 | hooks: 7 | # - id: trailing-whitespace 8 | # - id: end-of-file-fixer 9 | # - id: check-yaml 10 | - id: check-added-large-files 11 | - repo: https://github.com/psf/black 12 | rev: 24.2.0 13 | hooks: 14 | - id: black 15 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 1 | cff-version: 1.1.0 2 | message: "If you use this software, please cite the accompanying paper." 3 | abstract: "Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project." 4 | authors: 5 | - 6 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA" 7 | family-names: Savitzky 8 | given-names: "Benjamin H." 9 | - 10 | affiliation: "Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA" 11 | family-names: Zeltmann 12 | given-names: "Steven E. " 13 | - 14 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA" 15 | family-names: Hughes 16 | given-names: "Lauren A." 17 | - 18 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA" 19 | family-names: Brown 20 | given-names: "Hamish G." 21 | - 22 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA and Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA" 23 | family-names: Zhao 24 | given-names: Shiteng 25 | - 26 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA and Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA" 27 | family-names: Pelz 28 | given-names: "Philipp M." 29 | - 30 | affiliation: "Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany" 31 | family-names: Pekin 32 | given-names: "Thomas C." 33 | - 34 | affiliation: "Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA" 35 | family-names: Barnard 36 | given-names: "Edward S." 37 | - 38 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA" 39 | family-names: Donohue 40 | given-names: Jennifer 41 | - 42 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA" 43 | family-names: "Rangel DaCosta" 44 | given-names: Luis 45 | - 46 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA" 47 | family-names: Kennedy 48 | given-names: Ellis 49 | - 50 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA" 51 | family-names: Xie 52 | given-names: Yujun 53 | - 54 | affiliation: "Los Alamos National Laboratory, Los Alamos, NM 87545, USA" 55 | family-names: Janish 56 | given-names: "Matthew T." 57 | - 58 | affiliation: "Los Alamos National Laboratory, Los Alamos, NM 87545, USA" 59 | family-names: Schneider 60 | given-names: "Matthew M." 61 | - 62 | affiliation: "Toyota Research Institute, Los Altos, CA 94022, USA" 63 | family-names: Herring 64 | given-names: Patrick 65 | - 66 | affiliation: "Toyota Research Institute, Los Altos, CA 94022, USA" 67 | family-names: Gopal 68 | given-names: Chirranjeevi 69 | - 70 | affiliation: "Toyota Research Institute, Los Altos, CA 94022, USA" 71 | family-names: Anapolsky 72 | given-names: Abraham 73 | - 74 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA" 75 | family-names: Dhall 76 | given-names: Rohan 77 | - 78 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA" 79 | family-names: Bustillo 80 | given-names: "Karen C." 81 | - 82 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA" 83 | family-names: Ercius 84 | given-names: Peter 85 | - 86 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA" 87 | family-names: Scott 88 | given-names: "Mary C." 89 | - 90 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA" 91 | family-names: Ciston 92 | given-names: Jim 93 | - 94 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA" 95 | family-names: Minor 96 | given-names: "Andrew M." 97 | - 98 | affiliation: "National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA" 99 | family-names: Ophus 100 | given-names: Colin 101 | title: "py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis" 102 | version: 0.12.6 103 | doi: 10.1017/S1431927621000477 104 | date-released: 2021-05-21 105 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | # The `py4DSTEM` GUI 3 | 4 | This repository hosts the `pyqt` based graphical 4D--STEM data browser that was originally part of **py4DSTEM** until version 0.13.11. 5 | 6 | ## Installation 7 | The GUI is available on PyPI and conda-forge: 8 | 9 | `pip install py4D-browser` 10 | 11 | `conda install -c conda-forge py4d-browser` 12 | 13 | 14 | ## Usage 15 | Run `py4DGUI` in your terminal to open the GUI. Then just drag and drop a 4D-STEM dataset into the window! 16 | 17 | ### Controls 18 | * Move the virtual detector and the real-space selector using the mouse or using the keyboard shortcuts: WASD moves the detector and IJKL moves the selector, and holding down shift moves 5 pixels at a time. 19 | * Auto scaling of both views is on by default. Press the "Autoscale" buttons in the bottom right to disable. Press either button to apply automatic scaling once, or Shift + click to lock autoscaling back on. 20 | * Different shapes of virtual detector are available in the "Detector Shape" menu, and different detector responses are available in the "Detector Response" menu. 21 | * The information in the bottom bar contains the details of the virtual detector used to generate the images, and can be entered into py4DSTEM to generate the same image. 22 | * The FFT pane can be switched between displaying the FFT of the virtual image and displaying the [exit wave power cepstrum](https://doi.org/10.1016/j.ultramic.2020.112994). 23 | * Virtual images can be exported either as the scaled and clipped displays shown in the GUI or as raw data. The exact datatype stored in the raw TIFF image depends on both the datatype of the dataset and the type of virtual image being displayed (in particular, integer datatypes are converted internally to floating point to prevent overflows when generating any synthesized virtual images). 24 | * If the [EMPAD-G2 Raw Reader](https://github.com/sezelt/empad2) is installed in the same environment, an extra menu will appear that allows the concatenated binary format data to be background subtracted and calibrated in the GUI. You can also save the calibrated data as an HDF5 file for later analysis. 25 | 26 | ![Demonstration](/images/demo.gif) 27 | 28 | The keyboard map in the Help menu was made using [this tool](https://archie-adams.github.io/keyboard-shortcut-map-maker/) and the map file is in the top level of this repo. 29 | 30 | ## About 31 | 32 | ![py4DSTEM logo](/images/py4DSTEM_logo.png) 33 | 34 | **py4DSTEM** is an open source set of python tools for processing and analysis of four-dimensional scanning transmission electron microscopy (4D-STEM) data. Additional information: 35 | 36 | - [Our open access py4DSTEM publication in Microscopy and Microanalysis](https://doi.org/10.1017/S1431927621000477) describing this project and demonstrating a variety of applications. 37 | - [The py4DSTEM documentation pages](https://py4dstem.readthedocs.io/en/latest/index.html). 38 | - [Our open access 4D-STEM review in Microscopy and Microanalysis](https://doi.org/10.1017/S1431927619000497) describing this project and demonstrating a variety of applications. 39 | 40 | 41 | ### License 42 | 43 | GNU GPLv3 44 | 45 | **py4DSTEM** is open source software distributed under a GPLv3 license. 46 | It is free to use, alter, or build on, provided that any work derived from **py4DSTEM** is also kept free and open. 47 | -------------------------------------------------------------------------------- /images/demo.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/py4dstem/py4D-browser/eb33d15d7675d749e24df67bac890914c067ac83/images/demo.gif -------------------------------------------------------------------------------- /images/py4DSTEM_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/py4dstem/py4D-browser/eb33d15d7675d749e24df67bac890914c067ac83/images/py4DSTEM_logo.png -------------------------------------------------------------------------------- /py4DGUI-keymap.html: -------------------------------------------------------------------------------- 1 | py4DGUI-keymap.html

Keyboard Shortcut Map Maker

py4DGUI-keymap.html

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693 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["setuptools>=61.0"] 3 | build-backend = "setuptools.build_meta" 4 | 5 | [project] 6 | name = "py4D_browser" 7 | version = "1.2.1" 8 | authors = [ 9 | { name="Steven Zeltmann", email="steven.zeltmann@lbl.gov" }, 10 | ] 11 | description = "A 4D-STEM data browser built on py4DSTEM." 12 | readme = "README.md" 13 | requires-python = ">=3.10" 14 | classifiers = [ 15 | "Programming Language :: Python :: 3", 16 | "Operating System :: OS Independent", 17 | ] 18 | dependencies = [ 19 | "py4dstem >= 0.14.9", 20 | "emdfile >= 0.0.11", 21 | "h5py", 22 | "numpy >= 1.19", 23 | "matplotlib >= 3.2.2", 24 | "platformdirs", 25 | "PyQt5 >= 5.10", 26 | "pyqtgraph >= 0.11", 27 | "sigfig", 28 | ] 29 | 30 | [project.scripts] 31 | py4DGUI = "py4D_browser.runGUI:launch" 32 | 33 | [project.urls] 34 | "Homepage" = "https://github.com/py4dstem/py4D-browser" 35 | "Bug Tracker" = "https://github.com/py4dstem/py4D-browser/issues" 36 | 37 | [tool.pyright] 38 | venv = "py4dstem" 39 | 40 | [tool.setuptools] 41 | include-package-data = true 42 | 43 | [tool.setuptools.packages.find] 44 | where = ["src"] 45 | 46 | [tool.setuptools.package-data] 47 | py4D_browser = ["*.png"] 48 | -------------------------------------------------------------------------------- /src/py4D_browser/__init__.py: -------------------------------------------------------------------------------- 1 | from py4D_browser.main_window import DataViewer 2 | -------------------------------------------------------------------------------- /src/py4D_browser/dialogs.py: -------------------------------------------------------------------------------- 1 | from py4DSTEM import DataCube, data 2 | import pyqtgraph as pg 3 | import numpy as np 4 | from tqdm import tqdm 5 | from PyQt5.QtWidgets import QFrame, QPushButton, QApplication, QLabel 6 | from PyQt5.QtCore import pyqtSignal 7 | from PyQt5.QtCore import Qt, QObject 8 | from PyQt5.QtGui import QDoubleValidator 9 | from PyQt5.QtWidgets import ( 10 | QDialog, 11 | QHBoxLayout, 12 | QVBoxLayout, 13 | QSpinBox, 14 | QLineEdit, 15 | QComboBox, 16 | QGroupBox, 17 | QGridLayout, 18 | QCheckBox, 19 | ) 20 | from py4D_browser.utils import make_detector, StatusBarWriter 21 | 22 | 23 | class ResizeDialog(QDialog): 24 | def __init__(self, size, parent=None): 25 | super().__init__(parent=parent) 26 | 27 | self.new_size = size 28 | Nmax = size[0] * size[1] 29 | 30 | layout = QVBoxLayout(self) 31 | 32 | layout.addWidget(QLabel("Dataset size unknown. Please enter the shape:")) 33 | 34 | box_layout = QHBoxLayout() 35 | box_layout.addWidget(QLabel("X:")) 36 | 37 | xbox = QSpinBox() 38 | xbox.setRange(1, Nmax) 39 | xbox.setSingleStep(1) 40 | xbox.setKeyboardTracking(False) 41 | xbox.valueChanged.connect(self.x_box_changed) 42 | box_layout.addWidget(xbox) 43 | 44 | box_layout.addStretch() 45 | box_layout.addWidget(QLabel("Y:")) 46 | 47 | ybox = QSpinBox() 48 | ybox.setRange(1, Nmax) 49 | ybox.setSingleStep(1) 50 | ybox.setValue(Nmax) 51 | ybox.setKeyboardTracking(False) 52 | ybox.valueChanged.connect(self.y_box_changed) 53 | box_layout.addWidget(ybox) 54 | 55 | layout.addLayout(box_layout) 56 | 57 | button_layout = QHBoxLayout() 58 | button_layout.addStretch() 59 | done_button = QPushButton("Done") 60 | done_button.pressed.connect(self.close) 61 | button_layout.addWidget(done_button) 62 | layout.addLayout(button_layout) 63 | 64 | self.x_box = xbox 65 | self.y_box = ybox 66 | self.x_box_last = xbox.value() 67 | self.y_box_last = ybox.value() 68 | self.N = Nmax 69 | 70 | self.resize(600, 400) 71 | 72 | @classmethod 73 | def get_new_size(cls, size, parent=None): 74 | dialog = cls(size=size, parent=parent) 75 | dialog.exec_() 76 | return dialog.new_size 77 | 78 | def x_box_changed(self, new_value): 79 | if new_value == self.x_box_last: 80 | return 81 | x_new, y_new = self.get_next_rect( 82 | new_value, "down" if new_value < self.x_box_last else "up" 83 | ) 84 | 85 | self.x_box_last = x_new 86 | self.y_box_last = y_new 87 | 88 | self.x_box.setValue(x_new) 89 | self.y_box.setValue(y_new) 90 | 91 | self.new_size = [x_new, y_new] 92 | 93 | def y_box_changed(self, new_value): 94 | if new_value == self.y_box_last: 95 | return 96 | y_new, x_new = self.get_next_rect( 97 | new_value, "down" if new_value < self.y_box_last else "up" 98 | ) 99 | 100 | self.x_box_last = x_new 101 | self.y_box_last = y_new 102 | 103 | self.x_box.setValue(x_new) 104 | self.y_box.setValue(y_new) 105 | 106 | self.new_size = [x_new, y_new] 107 | 108 | def get_next_rect(self, current, direction): 109 | # get the next perfect rectangle 110 | iterator = ( 111 | range(current, 0, -1) if direction == "down" else range(current, self.N + 1) 112 | ) 113 | 114 | for i in iterator: 115 | if self.N % i == 0: 116 | return i, self.N // i 117 | 118 | raise ValueError("Factor finding failed, frustratingly.") 119 | 120 | 121 | class CalibrateDialog(QDialog): 122 | def __init__(self, datacube, parent, diffraction_selector_size=None): 123 | super().__init__(parent=parent) 124 | 125 | self.datacube = datacube 126 | self.parent = parent 127 | self.diffraction_selector_size = diffraction_selector_size 128 | 129 | layout = QVBoxLayout(self) 130 | 131 | ####### LAYOUT ######## 132 | 133 | realspace_box = QGroupBox("Real Space") 134 | layout.addWidget(realspace_box) 135 | realspace_layout = QHBoxLayout() 136 | realspace_box.setLayout(realspace_layout) 137 | 138 | realspace_left_layout = QGridLayout() 139 | realspace_layout.addLayout(realspace_left_layout) 140 | 141 | realspace_left_layout.addWidget(QLabel("Pixel Size"), 0, 0, Qt.AlignRight) 142 | self.realspace_pix_box = QLineEdit() 143 | self.realspace_pix_box.setValidator(QDoubleValidator()) 144 | realspace_left_layout.addWidget(self.realspace_pix_box, 0, 1) 145 | 146 | realspace_left_layout.addWidget(QLabel("Full Width"), 1, 0, Qt.AlignRight) 147 | self.realspace_fov_box = QLineEdit() 148 | realspace_left_layout.addWidget(self.realspace_fov_box, 1, 1) 149 | 150 | realspace_right_layout = QHBoxLayout() 151 | realspace_layout.addLayout(realspace_right_layout) 152 | self.realspace_unit_box = QComboBox() 153 | self.realspace_unit_box.addItems(["Å", "nm"]) 154 | self.realspace_unit_box.setMinimumContentsLength(5) 155 | realspace_right_layout.addWidget(self.realspace_unit_box) 156 | 157 | diff_box = QGroupBox("Diffraction") 158 | layout.addWidget(diff_box) 159 | diff_layout = QHBoxLayout() 160 | diff_box.setLayout(diff_layout) 161 | 162 | diff_left_layout = QGridLayout() 163 | diff_layout.addLayout(diff_left_layout) 164 | 165 | diff_left_layout.addWidget(QLabel("Pixel Size"), 0, 0, Qt.AlignRight) 166 | self.diff_pix_box = QLineEdit() 167 | diff_left_layout.addWidget(self.diff_pix_box, 0, 1) 168 | 169 | diff_left_layout.addWidget(QLabel("Full Width"), 1, 0, Qt.AlignRight) 170 | self.diff_fov_box = QLineEdit() 171 | diff_left_layout.addWidget(self.diff_fov_box, 1, 1) 172 | 173 | diff_left_layout.addWidget(QLabel("Selection Radius"), 2, 0, Qt.AlignRight) 174 | self.diff_selection_box = QLineEdit() 175 | diff_left_layout.addWidget(self.diff_selection_box, 2, 1) 176 | self.diff_selection_box.setEnabled(self.diffraction_selector_size is not None) 177 | 178 | diff_right_layout = QHBoxLayout() 179 | diff_layout.addLayout(diff_right_layout) 180 | self.diff_unit_box = QComboBox() 181 | self.diff_unit_box.setMinimumContentsLength(5) 182 | self.diff_unit_box.addItems( 183 | [ 184 | "mrad", 185 | "Å⁻¹", 186 | # "nm⁻¹", 187 | ] 188 | ) 189 | diff_right_layout.addWidget(self.diff_unit_box) 190 | 191 | button_layout = QHBoxLayout() 192 | button_layout.addStretch() 193 | cancel_button = QPushButton("Cancel") 194 | cancel_button.pressed.connect(self.close) 195 | button_layout.addWidget(cancel_button) 196 | done_button = QPushButton("Done") 197 | done_button.pressed.connect(self.set_and_close) 198 | button_layout.addWidget(done_button) 199 | layout.addLayout(button_layout) 200 | 201 | ######### CALLBACKS ######## 202 | self.realspace_pix_box.textEdited.connect(self.realspace_pix_box_changed) 203 | self.realspace_fov_box.textEdited.connect(self.realspace_fov_box_changed) 204 | self.diff_pix_box.textEdited.connect(self.diffraction_pix_box_changed) 205 | self.diff_fov_box.textEdited.connect(self.diffraction_fov_box_changed) 206 | self.diff_selection_box.textEdited.connect( 207 | self.diffraction_selection_box_changed 208 | ) 209 | 210 | def realspace_pix_box_changed(self, new_text): 211 | pix_size = float(new_text) 212 | 213 | fov = pix_size * self.datacube.R_Ny 214 | self.realspace_fov_box.setText(f"{fov:g}") 215 | 216 | def realspace_fov_box_changed(self, new_text): 217 | fov = float(new_text) 218 | 219 | pix_size = fov / self.datacube.R_Ny 220 | self.realspace_pix_box.setText(f"{pix_size:g}") 221 | 222 | def diffraction_pix_box_changed(self, new_text): 223 | pix_size = float(new_text) 224 | 225 | fov = pix_size * self.datacube.Q_Ny 226 | self.diff_fov_box.setText(f"{fov:g}") 227 | 228 | if self.diffraction_selector_size: 229 | sel_size = pix_size * self.diffraction_selector_size 230 | self.diff_selection_box.setText(f"{sel_size:g}") 231 | 232 | def diffraction_fov_box_changed(self, new_text): 233 | fov = float(new_text) 234 | 235 | pix_size = fov / self.datacube.Q_Ny 236 | self.diff_pix_box.setText(f"{pix_size:g}") 237 | 238 | if self.diffraction_selector_size: 239 | sel_size = pix_size * self.diffraction_selector_size 240 | self.diff_selection_box.setText(f"{sel_size:g}") 241 | 242 | def diffraction_selection_box_changed(self, new_text): 243 | if self.diffraction_selector_size: 244 | sel_size = float(new_text) 245 | 246 | pix_size = sel_size / self.diffraction_selector_size 247 | fov = pix_size * self.datacube.Q_Nx 248 | self.diff_pix_box.setText(f"{pix_size:g}") 249 | self.diff_fov_box.setText(f"{fov:g}") 250 | 251 | sel_size = pix_size * self.diffraction_selector_size 252 | self.diff_selection_box.setText(f"{sel_size:g}") 253 | 254 | def set_and_close(self): 255 | 256 | print("Old calibration") 257 | print(self.datacube.calibration) 258 | 259 | realspace_text = self.realspace_pix_box.text() 260 | if realspace_text != "": 261 | realspace_pix = float(realspace_text) 262 | self.datacube.calibration.set_R_pixel_size(realspace_pix) 263 | self.datacube.calibration.set_R_pixel_units( 264 | self.realspace_unit_box.currentText().replace("Å", "A") 265 | ) 266 | 267 | diff_text = self.diff_pix_box.text() 268 | if diff_text != "": 269 | diff_pix = float(diff_text) 270 | self.datacube.calibration.set_Q_pixel_size(diff_pix) 271 | translation = { 272 | "mrad": "mrad", 273 | "Å⁻¹": "A^-1", 274 | "nm⁻¹": "1/nm", 275 | } 276 | self.datacube.calibration.set_Q_pixel_units( 277 | translation[self.diff_unit_box.currentText()] 278 | ) 279 | 280 | self.parent.update_scalebars() 281 | 282 | print("New calibration") 283 | print(self.datacube.calibration) 284 | 285 | self.close() 286 | 287 | 288 | class ManualTCBFDialog(QDialog): 289 | def __init__(self, parent): 290 | super().__init__(parent=parent) 291 | 292 | self.parent = parent 293 | 294 | layout = QVBoxLayout(self) 295 | 296 | ####### LAYOUT ######## 297 | 298 | params_box = QGroupBox("Parameters") 299 | layout.addWidget(params_box) 300 | 301 | params_layout = QGridLayout() 302 | params_box.setLayout(params_layout) 303 | 304 | params_layout.addWidget(QLabel("Rotation [deg]"), 0, 0, Qt.AlignRight) 305 | self.rotation_box = QLineEdit() 306 | self.rotation_box.setValidator(QDoubleValidator()) 307 | params_layout.addWidget(self.rotation_box, 0, 1) 308 | 309 | params_layout.addWidget(QLabel("Transpose x/y"), 1, 0, Qt.AlignRight) 310 | self.transpose_box = QCheckBox() 311 | params_layout.addWidget(self.transpose_box, 1, 1) 312 | 313 | params_layout.addWidget(QLabel("Max Shift [px]"), 2, 0, Qt.AlignRight) 314 | self.max_shift_box = QLineEdit() 315 | self.max_shift_box.setValidator(QDoubleValidator()) 316 | params_layout.addWidget(self.max_shift_box, 2, 1) 317 | 318 | params_layout.addWidget(QLabel("Pad Images"), 3, 0, Qt.AlignRight) 319 | self.pad_checkbox = QCheckBox() 320 | params_layout.addWidget(self.pad_checkbox, 3, 1) 321 | 322 | button_layout = QHBoxLayout() 323 | button_layout.addStretch() 324 | cancel_button = QPushButton("Cancel") 325 | cancel_button.pressed.connect(self.close) 326 | button_layout.addWidget(cancel_button) 327 | done_button = QPushButton("Reconstruct") 328 | done_button.pressed.connect(self.reconstruct) 329 | button_layout.addWidget(done_button) 330 | layout.addLayout(button_layout) 331 | 332 | def reconstruct(self): 333 | datacube = self.parent.datacube 334 | 335 | # tcBF requires an area detector for generating the mask 336 | detector_shape = ( 337 | self.parent.detector_shape_group.checkedAction().text().replace("&", "") 338 | ) 339 | if detector_shape not in [ 340 | "Rectangular", 341 | "Circle", 342 | ]: 343 | self.parent.statusBar().showMessage( 344 | "tcBF requires a selection of the BF disk" 345 | ) 346 | return 347 | 348 | if detector_shape == "Rectangular": 349 | # Get slices corresponding to ROI 350 | slices, _ = self.parent.virtual_detector_roi.getArraySlice( 351 | self.parent.datacube.data[0, 0, :, :], 352 | self.parent.diffraction_space_widget.getImageItem(), 353 | ) 354 | slice_y, slice_x = slices 355 | 356 | mask = np.zeros( 357 | (self.parent.datacube.Q_Nx, self.parent.datacube.Q_Ny), dtype=np.bool_ 358 | ) 359 | mask[slice_x, slice_y] = True 360 | 361 | elif detector_shape == "Circle": 362 | R = self.parent.virtual_detector_roi.size()[0] / 2.0 363 | 364 | x0 = self.parent.virtual_detector_roi.pos()[0] + R 365 | y0 = self.parent.virtual_detector_roi.pos()[1] + R 366 | 367 | mask = make_detector( 368 | (self.parent.datacube.Q_Nx, self.parent.datacube.Q_Ny), 369 | "circle", 370 | ((x0, y0), R), 371 | ) 372 | else: 373 | raise ValueError("idk how we got here...") 374 | 375 | if self.max_shift_box.text() == "": 376 | self.parent.statusBar().showMessage("Max Shift must be specified") 377 | return 378 | 379 | rotation = np.radians(float(self.rotation_box.text() or 0.0)) 380 | transpose = self.transpose_box.checkState() 381 | max_shift = float(self.max_shift_box.text()) 382 | 383 | x, y = np.meshgrid( 384 | np.arange(datacube.Q_Nx), np.arange(datacube.Q_Ny), indexing="ij" 385 | ) 386 | 387 | mask_comx = np.sum(mask * x) / np.sum(mask) 388 | mask_comy = np.sum(mask * y) / np.sum(mask) 389 | 390 | pix_coord_x = x - mask_comx 391 | pix_coord_y = y - mask_comy 392 | 393 | q_pix = np.hypot(pix_coord_x, pix_coord_y) 394 | # unrotated shifts in scan pixels 395 | shifts_pix_x = pix_coord_x / np.max(q_pix * mask) * max_shift 396 | shifts_pix_y = pix_coord_y / np.max(q_pix * mask) * max_shift 397 | 398 | R = np.array( 399 | [ 400 | [np.cos(rotation), -np.sin(rotation)], 401 | [np.sin(rotation), np.cos(rotation)], 402 | ] 403 | ) 404 | T = np.array([[0.0, 1.0], [1.0, 0.0]]) 405 | 406 | if transpose: 407 | R = T @ R 408 | 409 | shifts_pix = np.stack([shifts_pix_x, shifts_pix_y], axis=2) @ R 410 | shifts_pix_x, shifts_pix_y = shifts_pix[..., 0], shifts_pix[..., 1] 411 | 412 | # generate image to accumulate reconstruction 413 | pad = self.pad_checkbox.checkState() 414 | pad_width = int( 415 | np.maximum(np.abs(shifts_pix_x).max(), np.abs(shifts_pix_y).max()) 416 | ) 417 | 418 | reconstruction = ( 419 | np.zeros((datacube.R_Nx + 2 * pad_width, datacube.R_Ny + 2 * pad_width)) 420 | if pad 421 | else np.zeros((datacube.R_Nx, datacube.R_Ny)) 422 | ) 423 | 424 | qx = np.fft.fftfreq(reconstruction.shape[0]) 425 | qy = np.fft.fftfreq(reconstruction.shape[1]) 426 | 427 | qx_operator, qy_operator = np.meshgrid(qx, qy, indexing="ij") 428 | qx_operator = qx_operator * -2.0j * np.pi 429 | qy_operator = qy_operator * -2.0j * np.pi 430 | 431 | # loop over images and shift 432 | img_indices = np.argwhere(mask) 433 | for mx, my in tqdm( 434 | img_indices, 435 | desc="Shifting images", 436 | file=StatusBarWriter(self.parent.statusBar()), 437 | mininterval=1.0, 438 | ): 439 | if mask[mx, my]: 440 | img_raw = datacube.data[:, :, mx, my] 441 | 442 | if pad: 443 | img = np.zeros_like(reconstruction) + img_raw.mean() 444 | img[ 445 | pad_width : img_raw.shape[0] + pad_width, 446 | pad_width : img_raw.shape[1] + pad_width, 447 | ] = img_raw 448 | else: 449 | img = img_raw 450 | 451 | reconstruction += np.real( 452 | np.fft.ifft2( 453 | np.fft.fft2(img) 454 | * np.exp( 455 | qx_operator * shifts_pix_x[mx, my] 456 | + qy_operator * shifts_pix_y[mx, my] 457 | ) 458 | ) 459 | ) 460 | 461 | # crop away padding so the image lines up with the original 462 | if pad: 463 | reconstruction = reconstruction[pad_width:-pad_width, pad_width:-pad_width] 464 | 465 | self.parent.set_virtual_image(reconstruction, reset=True) 466 | -------------------------------------------------------------------------------- /src/py4D_browser/empad2_reader.py: -------------------------------------------------------------------------------- 1 | import empad2 2 | from PyQt5.QtWidgets import QFileDialog, QMessageBox, QApplication 3 | import numpy as np 4 | from py4D_browser.utils import StatusBarWriter 5 | 6 | 7 | def set_empad2_sensor(self, sensor_name): 8 | self.empad2_calibrations = empad2.load_calibration_data(sensor=sensor_name) 9 | self.statusBar().showMessage(f"{sensor_name} calibrations loaded", 5_000) 10 | 11 | 12 | def load_empad2_background(self): 13 | if self.empad2_calibrations is not None: 14 | filename = raw_file_dialog(self) 15 | self.empad2_background = empad2.load_background( 16 | filepath=filename, calibration_data=self.empad2_calibrations 17 | ) 18 | self.statusBar().showMessage("Background data loaded", 5_000) 19 | else: 20 | QMessageBox.warning( 21 | self, "No calibrations loaded!", "Please select a sensor first" 22 | ) 23 | 24 | 25 | def load_empad2_dataset(self): 26 | if self.empad2_calibrations is not None: 27 | dummy_data = False 28 | if self.empad2_background is None: 29 | continue_wo_bkg = QMessageBox.question( 30 | self, 31 | "Load without background?", 32 | "Background data has not been loaded. Do you want to continue loading data?", 33 | ) 34 | if continue_wo_bkg == QMessageBox.No: 35 | return 36 | else: 37 | self.empad2_background = { 38 | "even": np.zeros((128, 128), dtype=np.float32), 39 | "odd": np.zeros((128, 128), dtype=np.float32), 40 | } 41 | dummy_data = True 42 | 43 | filename = raw_file_dialog(self) 44 | self.datacube = empad2.load_dataset( 45 | filename, 46 | self.empad2_background, 47 | self.empad2_calibrations, 48 | _tqdm_args={ 49 | "desc": "Loading", 50 | "file": StatusBarWriter(self.statusBar()), 51 | "mininterval": 1.0, 52 | }, 53 | ) 54 | 55 | if dummy_data: 56 | self.empad2_background = None 57 | 58 | self.update_diffraction_space_view(reset=True) 59 | self.update_real_space_view(reset=True) 60 | 61 | self.setWindowTitle(filename) 62 | 63 | else: 64 | QMessageBox.warning( 65 | self, "No calibrations loaded!", "Please select a sensor first" 66 | ) 67 | 68 | 69 | def raw_file_dialog(browser): 70 | filename = QFileDialog.getOpenFileName( 71 | browser, 72 | "Open EMPAD-G2 Data", 73 | "", 74 | "EMPAD-G2 Data (*.raw);;Any file(*)", 75 | ) 76 | if filename is not None and len(filename[0]) > 0: 77 | return filename[0] 78 | else: 79 | print("File was invalid, or something?") 80 | raise ValueError("Could not read file") 81 | -------------------------------------------------------------------------------- /src/py4D_browser/help_menu.py: -------------------------------------------------------------------------------- 1 | from PyQt5 import QtGui, QtCore 2 | from PyQt5.QtWidgets import ( 3 | QWidget, 4 | QDialog, 5 | QVBoxLayout, 6 | ) 7 | from pathlib import Path 8 | 9 | 10 | class KeyboardMapMenu(QDialog): 11 | def __init__(self, parent=None): 12 | super().__init__(parent=parent) 13 | 14 | self.keymap = QtGui.QPixmap( 15 | str(Path(__file__).parent.absolute() / "py4DGUI-keymap.png") 16 | ).scaledToWidth(1500) 17 | label = Label() 18 | 19 | label.setPixmap(self.keymap) 20 | 21 | layout = QVBoxLayout() 22 | layout.addWidget(label) 23 | self.setLayout(layout) 24 | 25 | self.resize(self.keymap.width(), self.keymap.height()) 26 | 27 | 28 | # Widget that smoothly resizes Pixmap keeping aspect ratio 29 | class Label(QWidget): 30 | def __init__(self, parent=None): 31 | QWidget.__init__(self, parent=parent) 32 | self.p = QtGui.QPixmap() 33 | 34 | def setPixmap(self, p): 35 | self.p = p 36 | self.update() 37 | 38 | def paintEvent(self, event): 39 | if not self.p.isNull(): 40 | painter = QtGui.QPainter(self) 41 | painter.setRenderHint(QtGui.QPainter.SmoothPixmapTransform) 42 | rect = self.rect() 43 | rect.setHeight(int(self.p.height() * rect.width() / self.p.width())) 44 | painter.drawPixmap(rect, self.p) 45 | -------------------------------------------------------------------------------- /src/py4D_browser/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/py4dstem/py4D-browser/eb33d15d7675d749e24df67bac890914c067ac83/src/py4D_browser/logo.png -------------------------------------------------------------------------------- /src/py4D_browser/main_window.py: -------------------------------------------------------------------------------- 1 | from PyQt5 import QtCore, QtGui 2 | from PyQt5.QtWidgets import ( 3 | QApplication, 4 | QMainWindow, 5 | QWidget, 6 | QMenu, 7 | QAction, 8 | QHBoxLayout, 9 | QSplitter, 10 | QActionGroup, 11 | QLabel, 12 | QToolTip, 13 | QPushButton, 14 | QShortcut, 15 | ) 16 | 17 | from matplotlib.backend_bases import tools 18 | import pyqtgraph as pg 19 | import numpy as np 20 | 21 | from functools import partial 22 | from pathlib import Path 23 | import importlib 24 | import os 25 | import platformdirs 26 | 27 | from py4D_browser.utils import pg_point_roi, VLine, LatchingButton 28 | from py4D_browser.scalebar import ScaleBar 29 | 30 | 31 | class DataViewer(QMainWindow): 32 | """ 33 | The class is used by instantiating and then entering the main Qt loop with, e.g.: 34 | app = DataViewer(sys.argv) 35 | app.exec_() 36 | """ 37 | 38 | LOG_SCALE_MIN_VALUE = 1e-6 39 | 40 | from py4D_browser.menu_actions import ( 41 | load_file, 42 | load_data_arina, 43 | load_data_auto, 44 | load_data_bin, 45 | load_data_mmap, 46 | show_file_dialog, 47 | get_savefile_name, 48 | export_datacube, 49 | export_virtual_image, 50 | show_keyboard_map, 51 | show_calibration_dialog, 52 | reshape_data, 53 | update_scalebars, 54 | reconstruct_tcBF_auto, 55 | reconstruct_tcBF_manual, 56 | ) 57 | 58 | from py4D_browser.update_views import ( 59 | set_virtual_image, 60 | set_diffraction_image, 61 | _render_virtual_image, 62 | _render_diffraction_image, 63 | update_diffraction_space_view, 64 | update_real_space_view, 65 | update_realspace_detector, 66 | update_diffraction_detector, 67 | set_diffraction_autoscale_range, 68 | set_real_space_autoscale_range, 69 | nudge_real_space_selector, 70 | nudge_diffraction_selector, 71 | update_annulus_pos, 72 | update_annulus_radii, 73 | update_tooltip, 74 | ) 75 | 76 | HAS_EMPAD2 = importlib.util.find_spec("empad2") is not None 77 | if HAS_EMPAD2: 78 | from py4D_browser.empad2_reader import ( 79 | set_empad2_sensor, 80 | load_empad2_background, 81 | load_empad2_dataset, 82 | ) 83 | 84 | def __init__(self, argv): 85 | super().__init__() 86 | # Define this as the QApplication object 87 | self.qtapp = QApplication.instance() 88 | if not self.qtapp: 89 | self.qtapp = QApplication(argv) 90 | 91 | self.setWindowTitle("py4DSTEM") 92 | 93 | icon = QtGui.QIcon(str(Path(__file__).parent.absolute() / "logo.png")) 94 | self.setWindowIcon(icon) 95 | self.qtapp.setWindowIcon(icon) 96 | 97 | self.setWindowTitle("py4DSTEM") 98 | self.setAcceptDrops(True) 99 | 100 | self.datacube = None 101 | 102 | # Load settings from cofig file 103 | config_path = os.path.join( 104 | platformdirs.user_config_dir("py4DGUI", "py4DSTEM"), "GUI_config.ini" 105 | ) 106 | print(f"Loading configuration from {config_path}") 107 | QtCore.QCoreApplication.setOrganizationName("py4DSTEM") 108 | QtCore.QCoreApplication.setOrganizationDomain("py4DSTEM.com") 109 | QtCore.QCoreApplication.setApplicationName("py4DGUI") 110 | self.settings = QtCore.QSettings(config_path, QtCore.QSettings.Format.IniFormat) 111 | 112 | # Reset stored state if so asked: 113 | if os.environ.get("PY4DGUI_RESET"): 114 | self.settings.remove("last_state") 115 | print("Cleared saved state, using defaults...") 116 | 117 | self.setup_menus() 118 | self.setup_views() 119 | 120 | # setup listener for tooltip 121 | self.tooltip_timer = pg.ThreadsafeTimer() 122 | self.tooltip_timer.timeout.connect(self.update_tooltip) 123 | self.tooltip_timer.start(1000 // 30) # run tooltip at 30 Hz 124 | font = QtGui.QFont(self.font()) 125 | font.setPointSize(10) 126 | QToolTip.setFont(font) 127 | 128 | self.resize( 129 | self.settings.value("last_state/window_size", QtCore.QSize(1000, 800)), 130 | ) 131 | 132 | self.show() 133 | 134 | # If a file was passed on the command line, open it 135 | if len(argv) > 1: 136 | self.load_file(argv[1]) 137 | 138 | # launch pyqtgraph's debug console if environment variable exists 139 | if os.environ.get("PY4DGUI_DEBUG"): 140 | pg.dbg() 141 | 142 | def setup_menus(self): 143 | self.menu_bar = self.menuBar() 144 | 145 | # File menu 146 | self.file_menu = QMenu("&File", self) 147 | self.menu_bar.addMenu(self.file_menu) 148 | 149 | import_label = QAction("Import", self) 150 | import_label.setDisabled(True) 151 | self.file_menu.addAction(import_label) 152 | 153 | self.load_auto_action = QAction("&Load Data...", self) 154 | self.load_auto_action.triggered.connect(self.load_data_auto) 155 | self.file_menu.addAction(self.load_auto_action) 156 | self.load_auto_action.setShortcut(QtGui.QKeySequence("Ctrl+O")) 157 | 158 | self.load_mmap_action = QAction("Load &Memory Map...", self) 159 | self.load_mmap_action.triggered.connect(self.load_data_mmap) 160 | self.file_menu.addAction(self.load_mmap_action) 161 | 162 | self.load_binned_action = QAction("Load Data &Binned...", self) 163 | self.load_binned_action.triggered.connect(self.load_data_bin) 164 | self.file_menu.addAction(self.load_binned_action) 165 | 166 | self.load_arina_action = QAction("Load &Arina Data...", self) 167 | self.load_arina_action.triggered.connect(self.load_data_arina) 168 | self.file_menu.addAction(self.load_arina_action) 169 | 170 | self.reshape_data_action = QAction("&Reshape Data...", self) 171 | self.reshape_data_action.triggered.connect(self.reshape_data) 172 | self.file_menu.addAction(self.reshape_data_action) 173 | 174 | self.file_menu.addSeparator() 175 | 176 | export_label = QAction("Export", self) 177 | export_label.setDisabled(True) 178 | self.file_menu.addAction(export_label) 179 | 180 | # Submenu to export datacube 181 | datacube_export_menu = QMenu("Export Datacube", self) 182 | self.file_menu.addMenu(datacube_export_menu) 183 | for method in ["Raw float32", "py4DSTEM HDF5", "Plain HDF5"]: 184 | menu_item = datacube_export_menu.addAction(method) 185 | menu_item.triggered.connect(partial(self.export_datacube, method)) 186 | if method == "py4DSTEM HDF5": 187 | menu_item.setShortcut(QtGui.QKeySequence("Ctrl+S")) 188 | 189 | # Submenu to export virtual image 190 | vimg_export_menu = QMenu("Export Virtual Image", self) 191 | self.file_menu.addMenu(vimg_export_menu) 192 | for method in ["PNG (display)", "TIFF (display)", "TIFF (raw)"]: 193 | menu_item = vimg_export_menu.addAction(method) 194 | menu_item.triggered.connect( 195 | partial(self.export_virtual_image, method, "image") 196 | ) 197 | 198 | # Submenu to export diffraction 199 | vdiff_export_menu = QMenu("Export Diffraction Pattern", self) 200 | self.file_menu.addMenu(vdiff_export_menu) 201 | for method in ["PNG (display)", "TIFF (display)", "TIFF (raw)"]: 202 | menu_item = vdiff_export_menu.addAction(method) 203 | menu_item.triggered.connect( 204 | partial(self.export_virtual_image, method, "diffraction") 205 | ) 206 | 207 | # EMPAD2 menu 208 | if self.HAS_EMPAD2: 209 | self.empad2_calibrations = None 210 | self.empad2_background = None 211 | 212 | self.empad2_menu = QMenu("&EMPAD-G2", self) 213 | self.menu_bar.addMenu(self.empad2_menu) 214 | 215 | sensor_menu = self.empad2_menu.addMenu("&Sensor") 216 | calibration_action_group = QActionGroup(self) 217 | calibration_action_group.setExclusive(True) 218 | from empad2 import SENSORS 219 | 220 | for name, sensor in SENSORS.items(): 221 | menu_item = sensor_menu.addAction(sensor["display-name"]) 222 | calibration_action_group.addAction(menu_item) 223 | menu_item.setCheckable(True) 224 | menu_item.triggered.connect(partial(self.set_empad2_sensor, name)) 225 | 226 | self.empad2_menu.addAction("Load &Background...").triggered.connect( 227 | self.load_empad2_background 228 | ) 229 | self.empad2_menu.addAction("Load &Dataset...").triggered.connect( 230 | self.load_empad2_dataset 231 | ) 232 | 233 | # Scaling Menu 234 | self.scaling_menu = QMenu("&Scaling", self) 235 | self.menu_bar.addMenu(self.scaling_menu) 236 | 237 | # Diffraction scaling 238 | diff_scaling_group = QActionGroup(self) 239 | diff_scaling_group.setExclusive(True) 240 | self.diff_scaling_group = diff_scaling_group 241 | diff_menu_separator = QAction("Diffraction", self) 242 | diff_menu_separator.setDisabled(True) 243 | self.scaling_menu.addAction(diff_menu_separator) 244 | 245 | diff_scale_linear_action = QAction("Linear", self) 246 | diff_scale_linear_action.setCheckable(True) 247 | diff_scale_linear_action.triggered.connect( 248 | partial(self._render_diffraction_image, True) 249 | ) 250 | diff_scaling_group.addAction(diff_scale_linear_action) 251 | self.scaling_menu.addAction(diff_scale_linear_action) 252 | 253 | diff_scale_log_action = QAction("Log", self) 254 | diff_scale_log_action.setCheckable(True) 255 | diff_scale_log_action.triggered.connect( 256 | partial(self._render_diffraction_image, True) 257 | ) 258 | diff_scaling_group.addAction(diff_scale_log_action) 259 | self.scaling_menu.addAction(diff_scale_log_action) 260 | 261 | diff_scale_sqrt_action = QAction("Square Root", self) 262 | diff_scale_sqrt_action.setCheckable(True) 263 | diff_scale_sqrt_action.triggered.connect( 264 | partial(self._render_diffraction_image, True) 265 | ) 266 | diff_scaling_group.addAction(diff_scale_sqrt_action) 267 | diff_scale_sqrt_action.setChecked(True) 268 | self.scaling_menu.addAction(diff_scale_sqrt_action) 269 | 270 | self.scaling_menu.addSeparator() 271 | 272 | # Real space scaling 273 | vimg_scaling_group = QActionGroup(self) 274 | vimg_scaling_group.setExclusive(True) 275 | self.vimg_scaling_group = vimg_scaling_group 276 | 277 | vimg_menu_separator = QAction("Virtual Image", self) 278 | vimg_menu_separator.setDisabled(True) 279 | self.scaling_menu.addAction(vimg_menu_separator) 280 | 281 | vimg_scale_linear_action = QAction("Linear", self) 282 | self.vimg_scale_linear_action = vimg_scale_linear_action # Save this one! 283 | vimg_scale_linear_action.setCheckable(True) 284 | vimg_scale_linear_action.setChecked(True) 285 | vimg_scale_linear_action.triggered.connect( 286 | partial(self._render_virtual_image, True) 287 | ) 288 | vimg_scaling_group.addAction(vimg_scale_linear_action) 289 | self.scaling_menu.addAction(vimg_scale_linear_action) 290 | 291 | vimg_scale_log_action = QAction("Log", self) 292 | vimg_scale_log_action.setCheckable(True) 293 | vimg_scale_log_action.triggered.connect( 294 | partial(self._render_virtual_image, True) 295 | ) 296 | vimg_scaling_group.addAction(vimg_scale_log_action) 297 | self.scaling_menu.addAction(vimg_scale_log_action) 298 | 299 | vimg_scale_sqrt_action = QAction("Square Root", self) 300 | vimg_scale_sqrt_action.setCheckable(True) 301 | vimg_scale_sqrt_action.triggered.connect( 302 | partial(self._render_virtual_image, True) 303 | ) 304 | vimg_scaling_group.addAction(vimg_scale_sqrt_action) 305 | self.scaling_menu.addAction(vimg_scale_sqrt_action) 306 | 307 | # Autorange menu 308 | self.autorange_menu = QMenu("&Autorange", self) 309 | self.menu_bar.addMenu(self.autorange_menu) 310 | 311 | diff_autoscale_separator = QAction("Diffraction", self) 312 | diff_autoscale_separator.setDisabled(True) 313 | self.autorange_menu.addAction(diff_autoscale_separator) 314 | 315 | diff_range_group = QActionGroup(self) 316 | diff_range_group.setExclusive(True) 317 | 318 | scale_range_default = self.settings.value( 319 | "last_state/diffraction_autorange", [0.1, 99.9], type=float 320 | ) 321 | for scale_range in [(0, 100), (0.1, 99.9), (1, 99), (2, 98), (5, 95)]: 322 | action = QAction(f"{scale_range[0]}% – {scale_range[1]}%", self) 323 | diff_range_group.addAction(action) 324 | self.autorange_menu.addAction(action) 325 | action.setCheckable(True) 326 | action.triggered.connect( 327 | partial(self.set_diffraction_autoscale_range, scale_range) 328 | ) 329 | # set default 330 | if ( 331 | scale_range[0] == scale_range_default[0] 332 | and scale_range[1] == scale_range_default[1] 333 | ): 334 | action.setChecked(True) 335 | self.set_diffraction_autoscale_range(scale_range, redraw=False) 336 | 337 | self.autorange_menu.addSeparator() 338 | 339 | vimg_autoscale_separator = QAction("Virtual Image", self) 340 | vimg_autoscale_separator.setDisabled(True) 341 | self.autorange_menu.addAction(vimg_autoscale_separator) 342 | 343 | vimg_range_group = QActionGroup(self) 344 | vimg_range_group.setExclusive(True) 345 | 346 | scale_range_default = self.settings.value( 347 | "last_state/realspace_autorange", [0.1, 99.9], type=float 348 | ) 349 | for scale_range in [(0, 100), (0.1, 99.9), (1, 99), (2, 98), (5, 95)]: 350 | action = QAction(f"{scale_range[0]}% – {scale_range[1]}%", self) 351 | vimg_range_group.addAction(action) 352 | self.autorange_menu.addAction(action) 353 | action.setCheckable(True) 354 | action.triggered.connect( 355 | partial(self.set_real_space_autoscale_range, scale_range) 356 | ) 357 | # set default 358 | if ( 359 | scale_range[0] == scale_range_default[0] 360 | and scale_range[1] == scale_range_default[1] 361 | ): 362 | action.setChecked(True) 363 | self.set_real_space_autoscale_range(scale_range, redraw=False) 364 | 365 | # Detector Response Menu 366 | self.detector_menu = QMenu("&Detector Response", self) 367 | self.menu_bar.addMenu(self.detector_menu) 368 | 369 | detector_mode_separator = QAction("Diffraction", self) 370 | detector_mode_separator.setDisabled(True) 371 | self.detector_menu.addAction(detector_mode_separator) 372 | 373 | detector_mode_group = QActionGroup(self) 374 | detector_mode_group.setExclusive(True) 375 | self.detector_mode_group = detector_mode_group 376 | 377 | detector_integrating_action = QAction("&Integrating", self) 378 | detector_integrating_action.setCheckable(True) 379 | detector_integrating_action.setChecked(True) 380 | detector_integrating_action.triggered.connect( 381 | partial(self.update_real_space_view, True) 382 | ) 383 | detector_mode_group.addAction(detector_integrating_action) 384 | self.detector_menu.addAction(detector_integrating_action) 385 | 386 | detector_maximum_action = QAction("&Maximum", self) 387 | detector_maximum_action.setCheckable(True) 388 | detector_maximum_action.triggered.connect( 389 | partial(self.update_real_space_view, True) 390 | ) 391 | detector_mode_group.addAction(detector_maximum_action) 392 | self.detector_menu.addAction(detector_maximum_action) 393 | 394 | detector_CoM = QAction("C&oM", self) 395 | detector_CoM.setCheckable(True) 396 | detector_CoM.triggered.connect(partial(self.update_real_space_view, True)) 397 | detector_mode_group.addAction(detector_CoM) 398 | self.detector_menu.addAction(detector_CoM) 399 | 400 | detector_CoMx = QAction("CoM &X", self) 401 | detector_CoMx.setCheckable(True) 402 | detector_CoMx.triggered.connect(partial(self.update_real_space_view, True)) 403 | detector_mode_group.addAction(detector_CoMx) 404 | self.detector_menu.addAction(detector_CoMx) 405 | 406 | detector_CoMy = QAction("CoM &Y", self) 407 | detector_CoMy.setCheckable(True) 408 | detector_CoMy.triggered.connect(partial(self.update_real_space_view, True)) 409 | detector_mode_group.addAction(detector_CoMy) 410 | self.detector_menu.addAction(detector_CoMy) 411 | 412 | detector_iCoM = QAction("i&CoM", self) 413 | detector_iCoM.setCheckable(True) 414 | detector_iCoM.triggered.connect(partial(self.update_real_space_view, True)) 415 | detector_mode_group.addAction(detector_iCoM) 416 | self.detector_menu.addAction(detector_iCoM) 417 | 418 | # Detector Response for realspace selector 419 | self.detector_menu.addSeparator() 420 | rs_detector_mode_separator = QAction("Virtual Image", self) 421 | rs_detector_mode_separator.setDisabled(True) 422 | self.detector_menu.addAction(rs_detector_mode_separator) 423 | 424 | realspace_detector_mode_group = QActionGroup(self) 425 | realspace_detector_mode_group.setExclusive(True) 426 | self.realspace_detector_mode_group = realspace_detector_mode_group 427 | 428 | detector_integrating_action = QAction("&Integrating", self) 429 | detector_integrating_action.setCheckable(True) 430 | detector_integrating_action.setChecked(True) 431 | detector_integrating_action.triggered.connect( 432 | partial(self.update_diffraction_space_view, True) 433 | ) 434 | realspace_detector_mode_group.addAction(detector_integrating_action) 435 | self.detector_menu.addAction(detector_integrating_action) 436 | 437 | detector_maximum_action = QAction("&Maximum", self) 438 | detector_maximum_action.setCheckable(True) 439 | detector_maximum_action.triggered.connect( 440 | partial(self.update_diffraction_space_view, True) 441 | ) 442 | realspace_detector_mode_group.addAction(detector_maximum_action) 443 | self.detector_menu.addAction(detector_maximum_action) 444 | 445 | # Detector Shape Menu 446 | self.detector_shape_menu = QMenu("Detector &Shape", self) 447 | self.menu_bar.addMenu(self.detector_shape_menu) 448 | 449 | detector_shape_group = QActionGroup(self) 450 | detector_shape_group.setExclusive(True) 451 | self.detector_shape_group = detector_shape_group 452 | 453 | diffraction_detector_separator = QAction("Diffraction", self) 454 | diffraction_detector_separator.setDisabled(True) 455 | self.detector_shape_menu.addAction(diffraction_detector_separator) 456 | 457 | detector_point_action = QAction("&Point", self) 458 | detector_point_action.setCheckable(True) 459 | detector_point_action.setChecked(True) # Default 460 | detector_point_action.triggered.connect(self.update_diffraction_detector) 461 | detector_shape_group.addAction(detector_point_action) 462 | self.detector_shape_menu.addAction(detector_point_action) 463 | 464 | detector_rectangle_action = QAction("&Rectangular", self) 465 | detector_rectangle_action.setCheckable(True) 466 | # detector_rectangle_action.setChecked(True) 467 | detector_rectangle_action.triggered.connect(self.update_diffraction_detector) 468 | detector_shape_group.addAction(detector_rectangle_action) 469 | self.detector_shape_menu.addAction(detector_rectangle_action) 470 | 471 | detector_circle_action = QAction("&Circle", self) 472 | detector_circle_action.setCheckable(True) 473 | detector_circle_action.triggered.connect(self.update_diffraction_detector) 474 | detector_shape_group.addAction(detector_circle_action) 475 | self.detector_shape_menu.addAction(detector_circle_action) 476 | 477 | detector_annulus_action = QAction("&Annulus", self) 478 | detector_annulus_action.setCheckable(True) 479 | detector_annulus_action.triggered.connect(self.update_diffraction_detector) 480 | detector_shape_group.addAction(detector_annulus_action) 481 | self.detector_shape_menu.addAction(detector_annulus_action) 482 | 483 | self.detector_shape_menu.addSeparator() 484 | 485 | diffraction_detector_separator = QAction("Virtual Image", self) 486 | diffraction_detector_separator.setDisabled(True) 487 | self.detector_shape_menu.addAction(diffraction_detector_separator) 488 | 489 | rs_detector_shape_group = QActionGroup(self) 490 | rs_detector_shape_group.setExclusive(True) 491 | self.rs_detector_shape_group = rs_detector_shape_group 492 | 493 | rs_detector_point_action = QAction("Poin&t", self) 494 | rs_detector_point_action.setCheckable(True) 495 | rs_detector_point_action.setChecked(True) # Default 496 | rs_detector_point_action.triggered.connect(self.update_realspace_detector) 497 | rs_detector_shape_group.addAction(rs_detector_point_action) 498 | self.detector_shape_menu.addAction(rs_detector_point_action) 499 | 500 | detector_rectangle_action = QAction("Rectan&gular", self) 501 | detector_rectangle_action.setCheckable(True) 502 | detector_rectangle_action.triggered.connect(self.update_realspace_detector) 503 | rs_detector_shape_group.addAction(detector_rectangle_action) 504 | self.detector_shape_menu.addAction(detector_rectangle_action) 505 | 506 | self.fft_menu = QMenu("FF&T View", self) 507 | self.menu_bar.addMenu(self.fft_menu) 508 | 509 | self.fft_source_action_group = QActionGroup(self) 510 | self.fft_source_action_group.setExclusive(True) 511 | img_fft_action = QAction("Virtual Image FFT", self) 512 | img_fft_action.setCheckable(True) 513 | img_fft_action.setChecked(True) 514 | img_fft_action.triggered.connect(partial(self.update_real_space_view, False)) 515 | self.fft_menu.addAction(img_fft_action) 516 | self.fft_source_action_group.addAction(img_fft_action) 517 | 518 | img_complex_fft_action = QAction("Virtual Image FFT (complex)", self) 519 | img_complex_fft_action.setCheckable(True) 520 | self.fft_menu.addAction(img_complex_fft_action) 521 | self.fft_source_action_group.addAction(img_complex_fft_action) 522 | img_complex_fft_action.triggered.connect( 523 | partial(self.update_real_space_view, False) 524 | ) 525 | 526 | img_ewpc_action = QAction("EWPC", self) 527 | img_ewpc_action.setCheckable(True) 528 | self.fft_menu.addAction(img_ewpc_action) 529 | self.fft_source_action_group.addAction(img_ewpc_action) 530 | img_ewpc_action.triggered.connect( 531 | partial(self.update_diffraction_space_view, False) 532 | ) 533 | 534 | # Processing menu 535 | self.processing_menu = QMenu("&Processing", self) 536 | self.menu_bar.addMenu(self.processing_menu) 537 | 538 | calibrate_action = QAction("&Calibrate...", self) 539 | calibrate_action.triggered.connect(self.show_calibration_dialog) 540 | self.processing_menu.addAction(calibrate_action) 541 | 542 | tcBF_action_manual = QAction("tcBF (Manual)...", self) 543 | tcBF_action_manual.triggered.connect(self.reconstruct_tcBF_manual) 544 | self.processing_menu.addAction(tcBF_action_manual) 545 | 546 | tcBF_action_auto = QAction("tcBF (Automatic)", self) 547 | tcBF_action_auto.triggered.connect(self.reconstruct_tcBF_auto) 548 | self.processing_menu.addAction(tcBF_action_auto) 549 | # tcBF_action_auto.setEnabled(False) 550 | 551 | # Help menu 552 | self.help_menu = QMenu("&Help", self) 553 | self.menu_bar.addMenu(self.help_menu) 554 | 555 | self.keyboard_map_action = QAction("Show &Keyboard Map", self) 556 | self.keyboard_map_action.triggered.connect(self.show_keyboard_map) 557 | self.help_menu.addAction(self.keyboard_map_action) 558 | 559 | def setup_views(self): 560 | # Set up the diffraction space window. 561 | self.diffraction_space_widget = pg.ImageView() 562 | self.diffraction_space_widget.setImage(np.zeros((512, 512))) 563 | 564 | self.diffraction_space_widget.setMouseTracking(True) 565 | 566 | # Create virtual detector ROI selector 567 | self.update_diffraction_detector() 568 | 569 | # Scalebar 570 | self.diffraction_scale_bar = ScaleBar(pixel_size=1, units="px", width=10) 571 | self.diffraction_scale_bar.setParentItem( 572 | self.diffraction_space_widget.getView() 573 | ) 574 | self.diffraction_scale_bar.anchor((1, 1), (1, 1), offset=(-40, -40)) 575 | 576 | # Name and return 577 | self.diffraction_space_widget.setWindowTitle("Diffraction Space") 578 | 579 | # Set up the real space window. 580 | self.real_space_widget = pg.ImageView() 581 | self.real_space_widget.setImage(np.zeros((512, 512))) 582 | 583 | # Add point selector connected to displayed diffraction pattern 584 | self.update_realspace_detector() 585 | 586 | # Scalebar, None by default 587 | self.real_space_scale_bar = ScaleBar(pixel_size=1, units="px", width=10) 588 | self.real_space_scale_bar.setParentItem(self.real_space_widget.getView()) 589 | self.real_space_scale_bar.anchor((1, 1), (1, 1), offset=(-40, -40)) 590 | 591 | # Name and return 592 | self.real_space_widget.setWindowTitle("Virtual Image") 593 | 594 | self.diffraction_space_widget.setAcceptDrops(True) 595 | self.real_space_widget.setAcceptDrops(True) 596 | self.diffraction_space_widget.dragEnterEvent = self.dragEnterEvent 597 | self.real_space_widget.dragEnterEvent = self.dragEnterEvent 598 | self.diffraction_space_widget.dropEvent = self.dropEvent 599 | self.real_space_widget.dropEvent = self.dropEvent 600 | 601 | # Set up the FFT window. 602 | self.fft_widget = pg.ImageView() 603 | self.fft_widget.setImage(np.zeros((512, 512))) 604 | 605 | # FFT scale bar 606 | self.fft_scale_bar = ScaleBar(pixel_size=1, units="1/px", width=10) 607 | self.fft_scale_bar.setParentItem(self.fft_widget.getView()) 608 | self.fft_scale_bar.anchor((1, 1), (1, 1), offset=(-40, -40)) 609 | 610 | # Name and return 611 | self.fft_widget.setWindowTitle("FFT of Virtual Image") 612 | self.fft_widget_text = pg.TextItem("FFT", (200, 200, 200), None, (0, 1)) 613 | self.fft_widget.addItem(self.fft_widget_text) 614 | 615 | self.fft_widget.setAcceptDrops(True) 616 | self.fft_widget.dragEnterEvent = self.dragEnterEvent 617 | self.fft_widget.dropEvent = self.dropEvent 618 | 619 | layout = QHBoxLayout() 620 | layout.addWidget(self.diffraction_space_widget, 1) 621 | 622 | # add a resizeable layout for the vimg and FFT 623 | rightside = QSplitter() 624 | rightside.addWidget(self.real_space_widget) 625 | rightside.addWidget(self.fft_widget) 626 | rightside.setOrientation(QtCore.Qt.Vertical) 627 | rightside.setStretchFactor(0, 2) 628 | layout.addWidget(rightside, 1) 629 | 630 | widget = QWidget() 631 | widget.setLayout(layout) 632 | self.setCentralWidget(widget) 633 | 634 | self.diffraction_space_widget.getView().setMenuEnabled(False) 635 | self.real_space_widget.getView().setMenuEnabled(False) 636 | self.fft_widget.getView().setMenuEnabled(False) 637 | 638 | # Setup Status Bar 639 | self.stats_button = QPushButton("Statistics") 640 | self.stats_menu = QMenu() 641 | 642 | self.realspace_title = QAction("Virtual Image") 643 | self.realspace_title.setDisabled(False) 644 | self.stats_menu.addAction(self.realspace_title) 645 | self.realspace_statistics_actions = [QAction("") for i in range(5)] 646 | for a in self.realspace_statistics_actions: 647 | self.stats_menu.addAction(a) 648 | 649 | self.stats_menu.addSeparator() 650 | 651 | self.diffraction_title = QAction("Diffraction") 652 | self.diffraction_title.setDisabled(False) 653 | self.stats_menu.addAction(self.diffraction_title) 654 | self.diffraction_statistics_actions = [QAction("") for i in range(5)] 655 | for a in self.diffraction_statistics_actions: 656 | self.stats_menu.addAction(a) 657 | 658 | self.stats_button.setMenu(self.stats_menu) 659 | 660 | self.cursor_value_text = QLabel("") 661 | self.diffraction_space_view_text = QLabel("Slice") 662 | self.real_space_view_text = QLabel("Scan Position") 663 | 664 | # self.statusBar().addPermanentWidget(VLine()) 665 | self.statusBar().addPermanentWidget(self.cursor_value_text) 666 | self.statusBar().addPermanentWidget(VLine()) 667 | self.statusBar().addPermanentWidget(self.stats_button) 668 | self.statusBar().addPermanentWidget(VLine()) 669 | self.statusBar().addPermanentWidget(self.diffraction_space_view_text) 670 | self.statusBar().addPermanentWidget(VLine()) 671 | self.statusBar().addPermanentWidget(self.real_space_view_text) 672 | self.statusBar().addPermanentWidget(VLine()) 673 | self.diffraction_rescale_button = LatchingButton( 674 | "Autorange Diffraction", 675 | status_bar=self.statusBar(), 676 | latched=True, 677 | ) 678 | self.diffraction_rescale_button.activated.connect( 679 | self.diffraction_space_widget.autoLevels 680 | ) 681 | self.statusBar().addPermanentWidget(self.diffraction_rescale_button) 682 | self.realspace_rescale_button = LatchingButton( 683 | "Autorange Virtual Image", 684 | status_bar=self.statusBar(), 685 | latched=True, 686 | ) 687 | self.realspace_rescale_button.activated.connect( 688 | self.real_space_widget.autoLevels 689 | ) 690 | self.statusBar().addPermanentWidget(self.realspace_rescale_button) 691 | 692 | def resizeEvent(self, event): 693 | # Store window size for next run 694 | self.settings.setValue("last_state/window_size", event.size()) 695 | 696 | # Handle dragging and dropping a file on the window 697 | def dragEnterEvent(self, event): 698 | if event.mimeData().hasUrls(): 699 | event.accept() 700 | else: 701 | event.ignore() 702 | 703 | def dropEvent(self, event): 704 | files = [u.toLocalFile() for u in event.mimeData().urls()] 705 | if len(files) == 1: 706 | print(f"Reieving dropped file: {files[0]}") 707 | self.load_file(files[0]) 708 | 709 | def keyPressEvent(self, event): 710 | key = event.key() 711 | modifier = event.modifiers() 712 | 713 | speed = 5 if modifier == QtCore.Qt.ShiftModifier else 1 714 | 715 | if key in [QtCore.Qt.Key_W, QtCore.Qt.Key_A, QtCore.Qt.Key_S, QtCore.Qt.Key_D]: 716 | self.nudge_diffraction_selector( 717 | dx=speed 718 | * ( 719 | -1 if key == QtCore.Qt.Key_W else 1 if key == QtCore.Qt.Key_S else 0 720 | ), 721 | dy=speed 722 | * ( 723 | -1 if key == QtCore.Qt.Key_A else 1 if key == QtCore.Qt.Key_D else 0 724 | ), 725 | ) 726 | elif key in [ 727 | QtCore.Qt.Key_I, 728 | QtCore.Qt.Key_J, 729 | QtCore.Qt.Key_K, 730 | QtCore.Qt.Key_L, 731 | ]: 732 | self.nudge_real_space_selector( 733 | dx=speed 734 | * ( 735 | -1 if key == QtCore.Qt.Key_I else 1 if key == QtCore.Qt.Key_K else 0 736 | ), 737 | dy=speed 738 | * ( 739 | -1 if key == QtCore.Qt.Key_J else 1 if key == QtCore.Qt.Key_L else 0 740 | ), 741 | ) 742 | -------------------------------------------------------------------------------- /src/py4D_browser/menu_actions.py: -------------------------------------------------------------------------------- 1 | from numbers import Real 2 | import py4DSTEM 3 | from PyQt5.QtWidgets import QFileDialog, QMessageBox 4 | import h5py 5 | import os 6 | import numpy as np 7 | import matplotlib.pyplot as plt 8 | from py4D_browser.help_menu import KeyboardMapMenu 9 | from py4D_browser.dialogs import CalibrateDialog, ResizeDialog, ManualTCBFDialog 10 | from py4D_browser.utils import make_detector 11 | from py4DSTEM.io.filereaders import read_arina 12 | 13 | 14 | def load_data_auto(self): 15 | filename = self.show_file_dialog() 16 | self.load_file(filename) 17 | 18 | 19 | def load_data_mmap(self): 20 | filename = self.show_file_dialog() 21 | self.load_file(filename, mmap=True) 22 | 23 | 24 | def load_data_bin(self): 25 | # TODO: Ask user for binning level 26 | filename = self.show_file_dialog() 27 | self.load_file(filename, mmap=False, binning=4) 28 | 29 | 30 | def load_data_arina(self): 31 | filename = self.show_file_dialog() 32 | dataset = read_arina(filename) 33 | 34 | # Warn if the data is not square 35 | if dataset.data.shape[1] == 1: 36 | self.statusBar().showMessage(f"Arina data was loaded as 3D, please reshape...") 37 | 38 | self.datacube = dataset 39 | self.diffraction_scale_bar.pixel_size = self.datacube.calibration.get_Q_pixel_size() 40 | self.diffraction_scale_bar.units = self.datacube.calibration.get_Q_pixel_units() 41 | 42 | self.real_space_scale_bar.pixel_size = self.datacube.calibration.get_R_pixel_size() 43 | self.real_space_scale_bar.units = self.datacube.calibration.get_R_pixel_units() 44 | 45 | self.fft_scale_bar.pixel_size = ( 46 | 1.0 / self.datacube.calibration.get_R_pixel_size() / self.datacube.R_Ny 47 | ) 48 | self.fft_scale_bar.units = f"1/{self.datacube.calibration.get_R_pixel_units()}" 49 | 50 | self.update_diffraction_space_view(reset=True) 51 | self.update_real_space_view(reset=True) 52 | 53 | self.setWindowTitle(filename) 54 | 55 | 56 | def load_file(self, filepath, mmap=False, binning=1): 57 | print(f"Loading file {filepath}") 58 | extension = os.path.splitext(filepath)[-1].lower() 59 | print(f"Type: {extension}") 60 | if extension in (".h5", ".hdf5", ".py4dstem", ".emd", ".mat"): 61 | file = h5py.File(filepath, "r") 62 | datacubes = get_ND(file) 63 | print(f"Found {len(datacubes)} 4D datasets inside the HDF5 file...") 64 | if len(datacubes) >= 1: 65 | # Read the first datacube in the HDF5 file into RAM 66 | print(f"Reading dataset at location {datacubes[0].name}") 67 | self.datacube = py4DSTEM.DataCube( 68 | datacubes[0] if mmap else datacubes[0][()] 69 | ) 70 | 71 | R_size, R_units, Q_size, Q_units = find_calibrations(datacubes[0]) 72 | 73 | self.datacube.calibration.set_R_pixel_size(R_size) 74 | self.datacube.calibration.set_R_pixel_units(R_units) 75 | self.datacube.calibration.set_Q_pixel_size(Q_size) 76 | self.datacube.calibration.set_Q_pixel_units(Q_units) 77 | 78 | else: 79 | # if no 4D data was found, look for 3D data 80 | datacubes = get_ND(file, N=3) 81 | print(f"Found {len(datacubes)} 3D datasets inside the HDF5 file...") 82 | if len(datacubes) >= 1: 83 | array = datacubes[0] if mmap else datacubes[0][()] 84 | new_shape = ResizeDialog.get_new_size([1, array.shape[0]], parent=self) 85 | self.datacube = py4DSTEM.DataCube( 86 | array.reshape(*new_shape, *array.shape[1:]) 87 | ) 88 | else: 89 | raise ValueError("No 4D (or even 3D) data detected in the H5 file!") 90 | elif extension in [".npy"]: 91 | self.datacube = py4DSTEM.DataCube(np.load(filepath)) 92 | else: 93 | self.datacube = py4DSTEM.import_file( 94 | filepath, 95 | mem="MEMMAP" if mmap else "RAM", 96 | binfactor=binning, 97 | ) 98 | 99 | self.update_scalebars() 100 | 101 | self.update_diffraction_space_view(reset=True) 102 | self.update_real_space_view(reset=True) 103 | 104 | self.setWindowTitle(filepath) 105 | 106 | 107 | def update_scalebars(self): 108 | 109 | realspace_translation = { 110 | "A": "Å", 111 | } 112 | reciprocal_translation = { 113 | "A^-1": "Å⁻¹", 114 | } 115 | 116 | self.diffraction_scale_bar.pixel_size = self.datacube.calibration.get_Q_pixel_size() 117 | q_units = self.datacube.calibration.get_Q_pixel_units() 118 | self.diffraction_scale_bar.units = ( 119 | reciprocal_translation[q_units] 120 | if q_units in reciprocal_translation.keys() 121 | else q_units 122 | ) 123 | 124 | self.real_space_scale_bar.pixel_size = self.datacube.calibration.get_R_pixel_size() 125 | r_units = self.datacube.calibration.get_R_pixel_units() 126 | self.real_space_scale_bar.units = ( 127 | realspace_translation[r_units] 128 | if r_units in realspace_translation.keys() 129 | else r_units 130 | ) 131 | 132 | self.fft_scale_bar.pixel_size = ( 133 | 1.0 / self.datacube.calibration.get_R_pixel_size() / self.datacube.R_Ny 134 | ) 135 | self.fft_scale_bar.units = f"{self.datacube.calibration.get_R_pixel_units()}⁻¹" 136 | 137 | self.diffraction_scale_bar.updateBar() 138 | self.real_space_scale_bar.updateBar() 139 | self.fft_scale_bar.updateBar() 140 | 141 | 142 | def reshape_data(self): 143 | new_shape = ResizeDialog.get_new_size(self.datacube.shape[:2], parent=self) 144 | self.datacube.data = self.datacube.data.reshape( 145 | *new_shape, *self.datacube.data.shape[2:] 146 | ) 147 | 148 | print(f"Reshaping data to {new_shape}") 149 | 150 | self.update_diffraction_space_view(reset=True) 151 | self.update_real_space_view(reset=True) 152 | 153 | 154 | def export_datacube(self, save_format: str): 155 | assert save_format in [ 156 | "Raw float32", 157 | "py4DSTEM HDF5", 158 | "Plain HDF5", 159 | ], f"unrecognized format {format}" 160 | assert self.datacube is not None, "No datacube!" 161 | 162 | # Display RAW format disclaimer 163 | if save_format == "Raw float32": 164 | response = QMessageBox.question( 165 | self, 166 | "Save RAW file?", 167 | ( 168 | "Saving raw binary files is not recommended as such files" 169 | " encode no information about the shape, endianness, or " 170 | "ordering of the data. Saving to HDF5 is recommended. " 171 | "Do you wish to continue saving RAW data?" 172 | ), 173 | QMessageBox.Cancel, 174 | QMessageBox.Save, 175 | ) 176 | 177 | if response == QMessageBox.Cancel: 178 | self.statusBar().showMessage("Cancelling due to user guilt", 5_000) 179 | return 180 | 181 | filename = self.get_savefile_name(save_format) 182 | 183 | if save_format == "Raw float32": 184 | self.datacube.data.astype(np.float32).tofile(filename) 185 | 186 | elif save_format == "py4DSTEM HDF5": 187 | py4DSTEM.save(filename, self.datacube, mode="o") 188 | 189 | elif save_format == "Plain HDF5": 190 | with h5py.File(filename, "w") as f: 191 | f["array"] = self.datacube.data 192 | 193 | 194 | def export_virtual_image(self, im_format: str, im_type: str): 195 | assert im_type in ["image", "diffraction"], f"bad image type: {im_type}" 196 | 197 | filename = self.get_savefile_name(im_format) 198 | 199 | view = ( 200 | self.real_space_widget if im_type == "image" else self.diffraction_space_widget 201 | ) 202 | 203 | vimg = view.image.T 204 | vmin, vmax = view.getLevels() 205 | 206 | if im_format == "PNG (display)": 207 | plt.imsave( 208 | fname=filename, arr=vimg, vmin=vmin, vmax=vmax, format="png", cmap="gray" 209 | ) 210 | elif im_format == "TIFF (display)": 211 | plt.imsave( 212 | fname=filename, arr=vimg, vmin=vmin, vmax=vmax, format="tiff", cmap="gray" 213 | ) 214 | elif im_format == "TIFF (raw)": 215 | from tifffile import TiffWriter 216 | 217 | vimg = ( 218 | self.unscaled_realspace_image 219 | if im_type == "image" 220 | else self.unscaled_diffraction_image 221 | ) 222 | with TiffWriter(filename) as tw: 223 | tw.write(vimg) 224 | else: 225 | raise RuntimeError("Nothing saved! Format not recognized") 226 | 227 | 228 | def show_keyboard_map(self): 229 | keymap = KeyboardMapMenu(parent=self) 230 | keymap.open() 231 | 232 | 233 | def reconstruct_tcBF_auto(self): 234 | # tcBF requires an area detector for generating the mask 235 | detector_shape = self.detector_shape_group.checkedAction().text().replace("&", "") 236 | if detector_shape not in [ 237 | "Rectangular", 238 | "Circle", 239 | ]: 240 | self.statusBar().showMessage("tcBF requires a selection of the BF disk", 5_000) 241 | return 242 | 243 | if ( 244 | self.datacube.calibration.get_R_pixel_units == "pixels" 245 | or self.datacube.calibration.get_Q_pixel_units == "pixels" 246 | ): 247 | self.statusBar().showMessage("tcBF requires caibrated data", 5_000) 248 | return 249 | 250 | if detector_shape == "Rectangular": 251 | # Get slices corresponding to ROI 252 | slices, _ = self.virtual_detector_roi.getArraySlice( 253 | self.datacube.data[0, 0, :, :], self.diffraction_space_widget.getImageItem() 254 | ) 255 | slice_y, slice_x = slices 256 | 257 | mask = np.zeros((self.datacube.Q_Nx, self.datacube.Q_Ny), dtype=np.bool_) 258 | mask[slice_x, slice_y] = True 259 | 260 | elif detector_shape == "Circle": 261 | R = self.virtual_detector_roi.size()[0] / 2.0 262 | 263 | x0 = self.virtual_detector_roi.pos()[0] + R 264 | y0 = self.virtual_detector_roi.pos()[1] + R 265 | 266 | mask = make_detector( 267 | (self.datacube.Q_Nx, self.datacube.Q_Ny), "circle", ((x0, y0), R) 268 | ) 269 | else: 270 | raise ValueError("idk how we got here...") 271 | 272 | # do tcBF! 273 | self.statusBar().showMessage("Reconstructing... (This may take a while)") 274 | self.app.processEvents() 275 | 276 | tcBF = py4DSTEM.process.phase.Parallax( 277 | energy=300e3, 278 | datacube=self.datacube, 279 | ) 280 | tcBF.preprocess( 281 | dp_mask=mask, 282 | plot_average_bf=False, 283 | vectorized_com_calculation=False, 284 | store_initial_arrays=False, 285 | ) 286 | tcBF.reconstruct( 287 | plot_aligned_bf=False, 288 | plot_convergence=False, 289 | ) 290 | 291 | self.set_virtual_image(tcBF.recon_BF, reset=True) 292 | 293 | 294 | def reconstruct_tcBF_manual(self): 295 | dialog = ManualTCBFDialog(parent=self) 296 | dialog.show() 297 | 298 | 299 | def show_calibration_dialog(self): 300 | # If the selector has a size, figure that out 301 | if hasattr(self, "virtual_detector_roi") and self.virtual_detector_roi is not None: 302 | selector_size = self.virtual_detector_roi.size()[0] / 2.0 303 | else: 304 | selector_size = None 305 | 306 | dialog = CalibrateDialog( 307 | self.datacube, parent=self, diffraction_selector_size=selector_size 308 | ) 309 | dialog.open() 310 | 311 | 312 | def show_file_dialog(self) -> str: 313 | filename = QFileDialog.getOpenFileName( 314 | self, 315 | "Open 4D-STEM Data", 316 | "", 317 | "4D-STEM Data (*.dm3 *.dm4 *.raw *.mib *.gtg *.h5 *.hdf5 *.emd *.py4dstem *.npy *.npz *.mat);;Any file (*)", 318 | ) 319 | if filename is not None and len(filename[0]) > 0: 320 | return filename[0] 321 | else: 322 | print("File was invalid, or something?") 323 | raise ValueError("Could not read file") 324 | 325 | 326 | def get_savefile_name(self, file_format) -> str: 327 | filters = { 328 | "Raw float32": "RAW File (*.raw *.f32);;Any file (*)", 329 | "py4DSTEM HDF5": "HDF5 File (*.hdf5 *.h5 *.emd *.py4dstem);;Any file (*)", 330 | "Plain HDF5": "HDF5 File (*.hdf5 *.h5;;Any file (*)", 331 | "PNG (display)": "PNG File (*.png);;Any file (*)", 332 | "TIFF (display)": "TIFF File (*.tiff *.tif *.tff);;Any File (*)", 333 | "TIFF (raw)": "TIFF File (*.tiff *.tif *.tff);;Any File (*)", 334 | } 335 | 336 | defaults = { 337 | "Raw float32": ".raw", 338 | "py4DSTEM HDF5": ".h5", 339 | "Plain HDF5": ".h5", 340 | "PNG (display)": ".png", 341 | "TIFF (display)": ".tiff", 342 | "TIFF (raw)": ".tiff", 343 | } 344 | 345 | file_filter = filters.get(file_format, "Any file (*)") 346 | 347 | filename = QFileDialog.getSaveFileName( 348 | parent=self, 349 | caption="Select save file", 350 | directory="", 351 | filter=file_filter, 352 | ) 353 | 354 | if filename is not None and len(filename[0]) > 0: 355 | fname = filename[0] 356 | print(f"Save file picked at {filename}") 357 | 358 | if os.path.splitext(fname)[1] == "": 359 | fname = fname + defaults.get(file_format, "") 360 | print(f"Added default extension to get: {fname}") 361 | return fname 362 | else: 363 | print("File was invalid, or something?") 364 | print(f"QFileDialog returned {filename}") 365 | raise ValueError("Could get save file") 366 | 367 | 368 | def get_ND(f, datacubes=None, N=4): 369 | # Traverse an h5py.File and look for Datasets with N dimensions 370 | if datacubes is None: 371 | datacubes = [] 372 | for k in f.keys(): 373 | if isinstance(f[k], h5py.Dataset): 374 | # we found data 375 | if len(f[k].shape) == N: 376 | datacubes.append(f[k]) 377 | elif isinstance(f[k], h5py.Group): 378 | get_ND(f[k], datacubes) 379 | return datacubes 380 | 381 | 382 | def find_calibrations(dset: h5py.Dataset): 383 | # Attempt to find calibrations from an H5 file 384 | R_size, R_units, Q_size, Q_units = 1.0, "pixels", 1.0, "pixels" 385 | 386 | # Does it look like a py4DSTEM file? 387 | try: 388 | if "emd_group_type" in dset.parent.attrs: 389 | # EMD files theoretically store this in the Array, 390 | # but in practice seem to only keep the calibrations 391 | # in the Metadata object, which is separate 392 | 393 | # R_size = dset.parent["dim0"][1] - dset.parent["dim0"][0] 394 | # R_units = dset.parent["dim0"].attrs["units"] 395 | 396 | # Q_size = dset.parent["dim3"][1] - dset.parent["dim3"][0] 397 | # Q_units = dset.parent["dim3"].attrs["units"] 398 | R_size = dset.parent.parent["metadatabundle"]["calibration"][ 399 | "R_pixel_size" 400 | ][()] 401 | R_units = dset.parent.parent["metadatabundle"]["calibration"][ 402 | "R_pixel_units" 403 | ][()].decode() 404 | 405 | Q_size = dset.parent.parent["metadatabundle"]["calibration"][ 406 | "Q_pixel_size" 407 | ][()] 408 | Q_units = dset.parent.parent["metadatabundle"]["calibration"][ 409 | "Q_pixel_units" 410 | ][()].decode() 411 | except: 412 | print( 413 | "This file looked like a py4DSTEM dataset but the dim vectors appear malformed..." 414 | ) 415 | 416 | # Does it look like an abTEM file? 417 | try: 418 | if "sampling" in dset.parent and "units" in dset.parent: 419 | R_size = dset.parent["sampling"][0] 420 | R_units = dset.parent["units"][0].decode().replace("Å", "A") 421 | 422 | Q_size = dset.parent["sampling"][3] 423 | Q_units = dset.parent["units"][3].decode() 424 | except: 425 | print( 426 | "This file looked like an abTEM simulation but the calibrations aren't as expected..." 427 | ) 428 | 429 | return R_size, R_units, Q_size, Q_units 430 | -------------------------------------------------------------------------------- /src/py4D_browser/py4DGUI-keymap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/py4dstem/py4D-browser/eb33d15d7675d749e24df67bac890914c067ac83/src/py4D_browser/py4DGUI-keymap.png -------------------------------------------------------------------------------- /src/py4D_browser/runGUI.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import py4D_browser 4 | import sys 5 | from PyQt5.QtWidgets import QApplication 6 | 7 | 8 | def launch(): 9 | app = QApplication(sys.argv) 10 | win = py4D_browser.DataViewer(sys.argv) 11 | win.show() 12 | sys.exit(app.exec_()) 13 | 14 | 15 | if __name__ == "__main__": 16 | launch() 17 | -------------------------------------------------------------------------------- /src/py4D_browser/scalebar.py: -------------------------------------------------------------------------------- 1 | from pyqtgraph import functions as fn 2 | from pyqtgraph import getConfigOption 3 | from pyqtgraph import Point 4 | from PyQt5 import QtCore, QtWidgets 5 | from pyqtgraph import GraphicsObject 6 | from pyqtgraph import GraphicsWidgetAnchor 7 | from pyqtgraph import TextItem 8 | import numpy as np 9 | from sigfig import round 10 | 11 | __all__ = ["ScaleBar"] 12 | 13 | 14 | class ScaleBar(GraphicsWidgetAnchor, GraphicsObject): 15 | """ 16 | Displays a rectangular bar to indicate the relative scale of objects on the view. 17 | """ 18 | 19 | def __init__( 20 | self, 21 | pixel_size: float, 22 | units: str, 23 | target_relaive_size=0.2, 24 | width=5, 25 | brush=None, 26 | pen=None, 27 | offset=None, 28 | nice_numbers=[1, 2, 5, 10], 29 | ): 30 | GraphicsObject.__init__(self) 31 | GraphicsWidgetAnchor.__init__(self) 32 | self.setFlag(self.GraphicsItemFlag.ItemHasNoContents) 33 | self.setAcceptedMouseButtons(QtCore.Qt.MouseButton.NoButton) 34 | 35 | if brush is None: 36 | brush = getConfigOption("foreground") 37 | self.brush = fn.mkBrush(brush) 38 | self.pen = fn.mkPen(pen) 39 | self._width = width 40 | self._target_relative_size = target_relaive_size 41 | self._nice_numbers = np.array(nice_numbers) 42 | 43 | self.pixel_size = pixel_size 44 | self.units = units 45 | 46 | if offset is None: 47 | offset = (0, 0) 48 | self.offset = offset 49 | 50 | self.bar = QtWidgets.QGraphicsRectItem() 51 | self.bar.setPen(self.pen) 52 | self.bar.setBrush(self.brush) 53 | self.bar.setParentItem(self) 54 | 55 | self.text = TextItem(text="smol", anchor=(0.5, 1)) 56 | self.text.setParentItem(self) 57 | 58 | def changeParent(self): 59 | view = self.parentItem() 60 | if view is None: 61 | return 62 | view.sigRangeChanged.connect(self.updateBar) 63 | self.updateBar() 64 | 65 | def updateBar(self): 66 | view = self.parentItem() 67 | 68 | if view is None: 69 | return 70 | 71 | view_width = view.viewRect().width() * self.pixel_size 72 | target_size = view_width * self._target_relative_size 73 | 74 | exponent = np.floor(np.log10(target_size)) 75 | mantissa = target_size / np.power(10, exponent) 76 | 77 | # Get the "nice" size of the scalebar 78 | nice_size = ( 79 | self._nice_numbers[np.argmin(np.abs(mantissa - self._nice_numbers))] 80 | * 10**exponent 81 | ) 82 | 83 | p1 = view.mapFromViewToItem(self, QtCore.QPointF(0, 0)) 84 | p2 = view.mapFromViewToItem( 85 | self, QtCore.QPointF(nice_size / self.pixel_size, 0) 86 | ) 87 | w = (p2 - p1).x() 88 | self.bar.setRect(QtCore.QRectF(-w, 0, w, self._width)) 89 | self.text.setPos(-w / 2.0, 0) 90 | self.text.setText(f"{round(nice_size,sigfigs=1,output_type=str)} {self.units}") 91 | 92 | def boundingRect(self): 93 | return QtCore.QRectF() 94 | 95 | def setParentItem(self, p): 96 | ret = GraphicsObject.setParentItem(self, p) 97 | if self.offset is not None: 98 | offset = Point(self.offset) 99 | anchorx = 1 if offset[0] <= 0 else 0 100 | anchory = 1 if offset[1] <= 0 else 0 101 | anchor = (anchorx, anchory) 102 | self.anchor(itemPos=anchor, parentPos=anchor, offset=offset) 103 | return ret 104 | -------------------------------------------------------------------------------- /src/py4D_browser/update_views.py: -------------------------------------------------------------------------------- 1 | import pyqtgraph as pg 2 | import numpy as np 3 | import py4DSTEM 4 | from functools import partial 5 | from PyQt5.QtWidgets import QApplication, QToolTip 6 | from PyQt5 import QtCore 7 | from PyQt5.QtGui import QCursor 8 | import os 9 | 10 | from py4D_browser.utils import ( 11 | pg_point_roi, 12 | make_detector, 13 | complex_to_Lab, 14 | StatusBarWriter, 15 | ) 16 | 17 | 18 | def update_real_space_view(self, reset=False): 19 | detector_shape = self.detector_shape_group.checkedAction().text().replace("&", "") 20 | assert detector_shape in [ 21 | "Point", 22 | "Rectangular", 23 | "Circle", 24 | "Annulus", 25 | ], detector_shape 26 | 27 | detector_mode = self.detector_mode_group.checkedAction().text().replace("&", "") 28 | assert detector_mode in [ 29 | "Integrating", 30 | "Maximum", 31 | "CoM", 32 | "CoM X", 33 | "CoM Y", 34 | "iCoM", 35 | ], detector_mode 36 | 37 | # If a CoM method is checked, ensure linear scaling 38 | scaling_mode = self.vimg_scaling_group.checkedAction().text().replace("&", "") 39 | if detector_mode == "CoM" and scaling_mode != "Linear": 40 | self.statusBar().showMessage("Warning! Setting linear scaling for CoM image") 41 | self.vimg_scale_linear_action.setChecked(True) 42 | scaling_mode = "Linear" 43 | 44 | if self.datacube is None: 45 | return 46 | 47 | # We will branch through certain combinations of detector shape and mode. 48 | # If we happen across a special case that can be handled directly, we 49 | # compute vimg. If we encounter a case that needs a more complicated 50 | # computation we compute the mask and then do the virtual image later 51 | mask = None 52 | if detector_shape == "Rectangular": 53 | # Get slices corresponding to ROI 54 | slices, transforms = self.virtual_detector_roi.getArraySlice( 55 | self.datacube.data[0, 0, :, :].T, 56 | self.diffraction_space_widget.getImageItem(), 57 | ) 58 | slice_y, slice_x = slices 59 | 60 | # update the label: 61 | self.diffraction_space_view_text.setText( 62 | f"Diffraction Slice: [{slice_x.start}:{slice_x.stop},{slice_y.start}:{slice_y.stop}]" 63 | ) 64 | 65 | if detector_mode == "Integrating": 66 | vimg = np.sum(self.datacube.data[:, :, slice_x, slice_y], axis=(2, 3)) 67 | elif detector_mode == "Maximum": 68 | vimg = np.max(self.datacube.data[:, :, slice_x, slice_y], axis=(2, 3)) 69 | else: 70 | mask = np.zeros((self.datacube.Q_Nx, self.datacube.Q_Ny), dtype=np.bool_) 71 | mask[slice_x, slice_y] = True 72 | 73 | elif detector_shape == "Circle": 74 | R = self.virtual_detector_roi.size()[0] / 2.0 75 | 76 | x0 = self.virtual_detector_roi.pos()[1] + R 77 | y0 = self.virtual_detector_roi.pos()[0] + R 78 | 79 | self.diffraction_space_view_text.setText( 80 | f"Diffraction Circle: Center ({x0:.0f},{y0:.0f}), Radius {R:.0f}" 81 | ) 82 | 83 | mask = make_detector( 84 | (self.datacube.Q_Nx, self.datacube.Q_Ny), "circle", ((x0, y0), R) 85 | ) 86 | elif detector_shape == "Annulus": 87 | inner_pos = self.virtual_detector_roi_inner.pos() 88 | inner_size = self.virtual_detector_roi_inner.size() 89 | R_inner = inner_size[0] / 2.0 90 | x0 = inner_pos[1] + R_inner 91 | y0 = inner_pos[0] + R_inner 92 | 93 | outer_size = self.virtual_detector_roi_outer.size() 94 | R_outer = outer_size[0] / 2.0 95 | 96 | if R_inner <= R_outer: 97 | R_inner -= 1 98 | 99 | self.diffraction_space_view_text.setText( 100 | f"Diffraction Annulus: Center ({x0:.0f},{y0:.0f}), Radii ({R_inner:.0f},{R_outer:.0f})" 101 | ) 102 | 103 | mask = make_detector( 104 | (self.datacube.Q_Nx, self.datacube.Q_Ny), 105 | "annulus", 106 | ((x0, y0), (R_inner, R_outer)), 107 | ) 108 | elif detector_shape == "Point": 109 | roi_state = self.virtual_detector_point.saveState() 110 | y0, x0 = roi_state["pos"] 111 | xc, yc = int(x0 + 1), int(y0 + 1) 112 | 113 | # Set the diffraction space image 114 | # Normalize coordinates 115 | xc = np.clip(xc, 0, self.datacube.Q_Nx - 1) 116 | yc = np.clip(yc, 0, self.datacube.Q_Ny - 1) 117 | vimg = self.datacube.data[:, :, xc, yc] 118 | 119 | self.diffraction_space_view_text.setText(f"Diffraction: Point [{xc},{yc}]") 120 | 121 | else: 122 | raise ValueError("Detector shape not recognized") 123 | 124 | if mask is not None: 125 | if "MASK_DEBUG" in os.environ: 126 | self.set_diffraction_image(mask.astype(np.float32), reset=reset) 127 | return 128 | mask = mask.astype(np.float32) 129 | vimg = np.zeros((self.datacube.R_Nx, self.datacube.R_Ny)) 130 | iterator = py4DSTEM.tqdmnd( 131 | self.datacube.R_Nx, 132 | self.datacube.R_Ny, 133 | file=StatusBarWriter(self.statusBar()), 134 | mininterval=0.1, 135 | ) 136 | 137 | if detector_mode == "Integrating": 138 | for rx, ry in iterator: 139 | vimg[rx, ry] = np.sum(self.datacube.data[rx, ry] * mask) 140 | 141 | elif detector_mode == "Maximum": 142 | for rx, ry in iterator: 143 | vimg[rx, ry] = np.max(self.datacube.data[rx, ry] * mask) 144 | 145 | elif "CoM" in detector_mode: 146 | ry_coord, rx_coord = np.meshgrid( 147 | np.arange(self.datacube.Q_Ny), np.arange(self.datacube.Q_Nx) 148 | ) 149 | CoMx = np.zeros_like(vimg) 150 | CoMy = np.zeros_like(vimg) 151 | for rx, ry in iterator: 152 | ar = self.datacube.data[rx, ry] * mask 153 | tot_intens = np.sum(ar) 154 | CoMx[rx, ry] = np.sum(rx_coord * ar) / tot_intens 155 | CoMy[rx, ry] = np.sum(ry_coord * ar) / tot_intens 156 | 157 | CoMx -= np.mean(CoMx) 158 | CoMy -= np.mean(CoMy) 159 | 160 | if detector_mode == "CoM": 161 | vimg = CoMx + 1.0j * CoMy 162 | elif detector_mode == "CoM X": 163 | vimg = CoMx 164 | elif detector_mode == "CoM Y": 165 | vimg = CoMy 166 | elif detector_mode == "iCoM": 167 | dpc = py4DSTEM.process.phase.DPC(verbose=False) 168 | dpc.preprocess( 169 | force_com_measured=[CoMx, CoMy], 170 | plot_rotation=False, 171 | plot_center_of_mass="", 172 | ) 173 | dpc.reconstruct(max_iter=1, step_size=1) 174 | vimg = dpc.object_phase 175 | else: 176 | raise ValueError("Mode logic gone haywire!") 177 | 178 | else: 179 | raise ValueError("Oopsie") 180 | 181 | self.set_virtual_image(vimg, reset=reset) 182 | 183 | 184 | def set_virtual_image(self, vimg, reset=False): 185 | self.unscaled_realspace_image = vimg 186 | self._render_virtual_image(reset=reset) 187 | 188 | 189 | def _render_virtual_image(self, reset=False): 190 | vimg = self.unscaled_realspace_image 191 | 192 | # for 2D images, use the scaling set by the user 193 | # for RGB (3D) images, always scale linear 194 | if np.isrealobj(vimg): 195 | scaling_mode = self.vimg_scaling_group.checkedAction().text().replace("&", "") 196 | assert scaling_mode in ["Linear", "Log", "Square Root"], scaling_mode 197 | 198 | if scaling_mode == "Linear": 199 | new_view = vimg.copy() 200 | elif scaling_mode == "Log": 201 | new_view = np.log2(np.maximum(vimg, self.LOG_SCALE_MIN_VALUE)) 202 | elif scaling_mode == "Square Root": 203 | new_view = np.sqrt(np.maximum(vimg, 0)) 204 | else: 205 | raise ValueError("Mode not recognized") 206 | 207 | auto_level = reset or self.realspace_rescale_button.latched 208 | 209 | self.real_space_widget.setImage( 210 | new_view.T, 211 | autoLevels=False, 212 | levels=( 213 | ( 214 | np.percentile(new_view, self.real_space_autoscale_percentiles[0]), 215 | np.percentile(new_view, self.real_space_autoscale_percentiles[1]), 216 | ) 217 | if auto_level 218 | else None 219 | ), 220 | autoRange=reset, 221 | ) 222 | else: 223 | new_view = complex_to_Lab(vimg) 224 | self.real_space_widget.setImage( 225 | np.transpose(new_view, (1, 0, 2)), # flip x/y but keep RGB ordering 226 | autoLevels=False, 227 | levels=(0, 1), 228 | autoRange=reset, 229 | ) 230 | 231 | stats_text = [ 232 | f"Min:\t{vimg.min():.5g}", 233 | f"Max:\t{vimg.max():.5g}", 234 | f"Mean:\t{vimg.mean():.5g}", 235 | f"Sum:\t{vimg.sum():.5g}", 236 | f"Std:\t{np.std(vimg):.5g}", 237 | ] 238 | 239 | for t, m in zip(stats_text, self.realspace_statistics_actions): 240 | m.setText(t) 241 | 242 | # Update FFT view 243 | self.unscaled_fft_image = None 244 | vimg_2D = vimg if np.isrealobj(vimg) else np.abs(vimg) 245 | fft_window = ( 246 | np.hanning(vimg_2D.shape[0])[:, None] * np.hanning(vimg_2D.shape[1])[None, :] 247 | ) 248 | if self.fft_source_action_group.checkedAction().text() == "Virtual Image FFT": 249 | fft = np.abs(np.fft.fftshift(np.fft.fft2(vimg_2D * fft_window))) ** 0.5 250 | levels = (np.min(fft), np.percentile(fft, 99.9)) 251 | mode_switch = self.fft_widget_text.textItem.toPlainText() != "Virtual Image FFT" 252 | self.fft_widget_text.setText("Virtual Image FFT") 253 | self.fft_widget.setImage( 254 | fft.T, autoLevels=False, levels=levels, autoRange=mode_switch 255 | ) 256 | self.fft_widget.getImageItem().setRect(0, 0, fft.shape[1], fft.shape[1]) 257 | if mode_switch: 258 | # Need to autorange after setRect 259 | self.fft_widget.autoRange() 260 | self.unscaled_fft_image = fft 261 | elif ( 262 | self.fft_source_action_group.checkedAction().text() 263 | == "Virtual Image FFT (complex)" 264 | ): 265 | fft = np.fft.fftshift(np.fft.fft2(vimg_2D * fft_window)) 266 | levels = (np.min(np.abs(fft)), np.percentile(np.abs(fft), 99.9)) 267 | mode_switch = self.fft_widget_text.textItem.toPlainText() != "Virtual Image FFT" 268 | self.fft_widget_text.setText("Virtual Image FFT") 269 | fft_img = complex_to_Lab( 270 | fft.T, 271 | amin=levels[0], 272 | amax=levels[1], 273 | ab_scale=128, 274 | gamma=0.5, 275 | ) 276 | self.fft_widget.setImage( 277 | fft_img, 278 | autoLevels=False, 279 | autoRange=mode_switch, 280 | levels=(0, 1), 281 | ) 282 | 283 | self.fft_widget.getImageItem().setRect(0, 0, fft.shape[1], fft.shape[1]) 284 | if mode_switch: 285 | # Need to autorange after setRect 286 | self.fft_widget.autoRange() 287 | self.unscaled_fft_image = fft 288 | 289 | 290 | def update_diffraction_space_view(self, reset=False): 291 | if self.datacube is None: 292 | return 293 | 294 | detector_shape = ( 295 | self.rs_detector_shape_group.checkedAction().text().replace("&", "") 296 | ) 297 | assert detector_shape in [ 298 | "Point", 299 | "Rectangular", 300 | ], detector_shape 301 | 302 | detector_response = ( 303 | self.realspace_detector_mode_group.checkedAction().text().replace("&", "") 304 | ) 305 | assert detector_response in ["Integrating", "Maximum"], detector_response 306 | 307 | if detector_shape == "Point": 308 | roi_state = self.real_space_point_selector.saveState() 309 | y0, x0 = roi_state["pos"] 310 | xc, yc = int(x0 + 1), int(y0 + 1) 311 | 312 | # Set the diffraction space image 313 | # Normalize coordinates 314 | xc = np.clip(xc, 0, self.datacube.R_Nx - 1) 315 | yc = np.clip(yc, 0, self.datacube.R_Ny - 1) 316 | 317 | self.real_space_view_text.setText(f"Virtual Image: Point [{xc},{yc}]") 318 | 319 | DP = self.datacube.data[xc, yc] 320 | elif detector_shape == "Rectangular": 321 | # Get slices corresponding to ROI 322 | slices, _ = self.real_space_rect_selector.getArraySlice( 323 | np.zeros((self.datacube.Rshape)).T, self.real_space_widget.getImageItem() 324 | ) 325 | slice_y, slice_x = slices 326 | 327 | # update the label: 328 | self.real_space_view_text.setText( 329 | f"Virtual Image: Slice [{slice_x.start}:{slice_x.stop},{slice_y.start}:{slice_y.stop}]" 330 | ) 331 | 332 | if detector_response == "Integrating": 333 | DP = np.sum(self.datacube.data[slice_x, slice_y], axis=(0, 1)) 334 | elif detector_response == "Maximum": 335 | DP = np.max(self.datacube.data[slice_x, slice_y], axis=(0, 1)) 336 | else: 337 | raise ValueError("Detector response problem") 338 | 339 | else: 340 | raise ValueError("Detector shape not recognized") 341 | 342 | self.set_diffraction_image(DP, reset=reset) 343 | 344 | 345 | def set_diffraction_image(self, DP, reset=False): 346 | self.unscaled_diffraction_image = DP 347 | self._render_diffraction_image(reset=reset) 348 | 349 | 350 | def _render_diffraction_image(self, reset=False): 351 | DP = self.unscaled_diffraction_image 352 | 353 | scaling_mode = self.diff_scaling_group.checkedAction().text().replace("&", "") 354 | assert scaling_mode in ["Linear", "Log", "Square Root"] 355 | 356 | if scaling_mode == "Linear": 357 | new_view = DP.copy() 358 | elif scaling_mode == "Log": 359 | new_view = np.log2(np.maximum(DP, self.LOG_SCALE_MIN_VALUE)) 360 | elif scaling_mode == "Square Root": 361 | new_view = np.sqrt(np.maximum(DP, 0)) 362 | else: 363 | raise ValueError("Mode not recognized") 364 | 365 | stats_text = [ 366 | f"Min:\t{DP.min():.5g}", 367 | f"Max:\t{DP.max():.5g}", 368 | f"Mean:\t{DP.mean():.5g}", 369 | f"Sum:\t{DP.sum():.5g}", 370 | f"Std:\t{np.std(DP):.5g}", 371 | ] 372 | 373 | for t, m in zip(stats_text, self.diffraction_statistics_actions): 374 | m.setText(t) 375 | 376 | auto_level = reset or self.diffraction_rescale_button.latched 377 | 378 | self.diffraction_space_widget.setImage( 379 | new_view.T, 380 | autoLevels=False, 381 | levels=( 382 | ( 383 | np.percentile(new_view, self.diffraction_autoscale_percentiles[0]), 384 | np.percentile(new_view, self.diffraction_autoscale_percentiles[1]), 385 | ) 386 | if auto_level 387 | else None 388 | ), 389 | autoRange=reset, 390 | ) 391 | 392 | if self.fft_source_action_group.checkedAction().text() == "EWPC": 393 | log_clip = np.maximum(1e-10, np.percentile(np.maximum(DP, 0.0), 0.1)) 394 | fft = np.abs(np.fft.fftshift(np.fft.fft2(np.log(np.maximum(DP, log_clip))))) 395 | levels = (np.min(fft), np.percentile(fft, 99.9)) 396 | mode_switch = self.fft_widget_text.textItem.toPlainText() != "EWPC" 397 | self.fft_widget_text.setText("EWPC") 398 | self.fft_widget.setImage( 399 | fft.T, autoLevels=False, levels=levels, autoRange=mode_switch 400 | ) 401 | 402 | 403 | def update_realspace_detector(self): 404 | # change the shape of the detector, then update the view 405 | 406 | detector_shape = ( 407 | self.rs_detector_shape_group.checkedAction().text().replace("&", "") 408 | ) 409 | assert detector_shape in ["Point", "Rectangular"], detector_shape 410 | 411 | main_pen = {"color": "g", "width": 6} 412 | handle_pen = {"color": "r", "width": 9} 413 | hover_pen = {"color": "c", "width": 6} 414 | hover_handle = {"color": "c", "width": 9} 415 | 416 | if self.datacube is None: 417 | x0, y0 = 0, 0 418 | xr, yr = 4, 4 419 | else: 420 | x, y = self.datacube.data.shape[2:] 421 | y0, x0 = x // 2, y // 2 422 | xr, yr = (np.minimum(x, y) / 10,) * 2 423 | 424 | # Remove existing detector 425 | if hasattr(self, "real_space_point_selector"): 426 | self.real_space_widget.view.scene().removeItem(self.real_space_point_selector) 427 | self.real_space_point_selector = None 428 | if hasattr(self, "real_space_rect_selector"): 429 | self.real_space_widget.view.scene().removeItem(self.real_space_rect_selector) 430 | self.real_space_rect_selector = None 431 | 432 | # Point detector 433 | if detector_shape == "Point": 434 | self.real_space_point_selector = pg_point_roi( 435 | self.real_space_widget.getView(), 436 | center=(x0 - 0.5, y0 - 0.5), 437 | pen=main_pen, 438 | hoverPen=hover_pen, 439 | ) 440 | self.real_space_point_selector.sigRegionChanged.connect( 441 | partial(self.update_diffraction_space_view, False) 442 | ) 443 | 444 | # Rectangular detector 445 | elif detector_shape == "Rectangular": 446 | self.real_space_rect_selector = pg.RectROI( 447 | [int(x0 - xr / 2), int(y0 - yr / 2)], 448 | [int(xr), int(yr)], 449 | pen=main_pen, 450 | handlePen=handle_pen, 451 | hoverPen=hover_pen, 452 | handleHoverPen=hover_handle, 453 | ) 454 | self.real_space_widget.getView().addItem(self.real_space_rect_selector) 455 | self.real_space_rect_selector.sigRegionChangeFinished.connect( 456 | partial(self.update_diffraction_space_view, False) 457 | ) 458 | 459 | else: 460 | raise ValueError("Unknown detector shape! Got: {}".format(detector_shape)) 461 | 462 | self.update_diffraction_space_view(reset=True) 463 | 464 | 465 | def update_diffraction_detector(self): 466 | # change the shape of the detector, then update the view 467 | 468 | detector_shape = self.detector_shape_group.checkedAction().text().strip("&") 469 | assert detector_shape in ["Point", "Rectangular", "Circle", "Annulus"] 470 | 471 | main_pen = {"color": "g", "width": 6} 472 | handle_pen = {"color": "r", "width": 9} 473 | hover_pen = {"color": "c", "width": 6} 474 | hover_handle = {"color": "c", "width": 9} 475 | 476 | if self.datacube is None: 477 | x0, y0 = 0, 0 478 | xr, yr = 4, 4 479 | else: 480 | x, y = self.datacube.data.shape[2:] 481 | y0, x0 = x // 2, y // 2 482 | xr, yr = (np.minimum(x, y) / 10,) * 2 483 | 484 | # Remove existing detector 485 | if hasattr(self, "virtual_detector_point"): 486 | self.diffraction_space_widget.view.scene().removeItem( 487 | self.virtual_detector_point 488 | ) 489 | self.virtual_detector_point = None 490 | if hasattr(self, "virtual_detector_roi"): 491 | self.diffraction_space_widget.view.scene().removeItem(self.virtual_detector_roi) 492 | self.virtual_detector_roi = None 493 | if hasattr(self, "virtual_detector_roi_inner"): 494 | self.diffraction_space_widget.view.scene().removeItem( 495 | self.virtual_detector_roi_inner 496 | ) 497 | self.virtual_detector_roi_inner = None 498 | if hasattr(self, "virtual_detector_roi_outer"): 499 | self.diffraction_space_widget.view.scene().removeItem( 500 | self.virtual_detector_roi_outer 501 | ) 502 | self.virtual_detector_roi_outer = None 503 | 504 | # Point detector 505 | if detector_shape == "Point": 506 | self.virtual_detector_point = pg_point_roi( 507 | self.diffraction_space_widget.getView(), 508 | center=(x0 - 0.5, y0 - 0.5), 509 | pen=main_pen, 510 | hoverPen=hover_pen, 511 | ) 512 | self.virtual_detector_point.sigRegionChanged.connect( 513 | partial(self.update_real_space_view, False) 514 | ) 515 | 516 | # Rectangular detector 517 | elif detector_shape == "Rectangular": 518 | self.virtual_detector_roi = pg.RectROI( 519 | [int(x0 - xr / 2), int(y0 - yr / 2)], 520 | [int(xr), int(yr)], 521 | pen=main_pen, 522 | handlePen=handle_pen, 523 | hoverPen=hover_pen, 524 | handleHoverPen=hover_handle, 525 | ) 526 | self.diffraction_space_widget.getView().addItem(self.virtual_detector_roi) 527 | self.virtual_detector_roi.sigRegionChangeFinished.connect( 528 | partial(self.update_real_space_view, False) 529 | ) 530 | 531 | # Circular detector 532 | elif detector_shape == "Circle": 533 | self.virtual_detector_roi = pg.CircleROI( 534 | [int(x0 - xr / 2), int(y0 - yr / 2)], 535 | [int(xr), int(yr)], 536 | pen=main_pen, 537 | handlePen=handle_pen, 538 | hoverPen=hover_pen, 539 | handleHoverPen=hover_handle, 540 | ) 541 | self.diffraction_space_widget.getView().addItem(self.virtual_detector_roi) 542 | self.virtual_detector_roi.sigRegionChangeFinished.connect( 543 | partial(self.update_real_space_view, False) 544 | ) 545 | 546 | # Annular dector 547 | elif detector_shape == "Annulus": 548 | # Make outer detector 549 | self.virtual_detector_roi_outer = pg.CircleROI( 550 | [int(x0 - xr), int(y0 - yr)], 551 | [int(2 * xr), int(2 * yr)], 552 | pen=main_pen, 553 | handlePen=handle_pen, 554 | hoverPen=hover_pen, 555 | handleHoverPen=hover_handle, 556 | ) 557 | self.diffraction_space_widget.getView().addItem(self.virtual_detector_roi_outer) 558 | 559 | # Make inner detector 560 | self.virtual_detector_roi_inner = pg.CircleROI( 561 | [int(x0 - xr / 2), int(y0 - yr / 2)], 562 | [int(xr), int(yr)], 563 | pen=main_pen, 564 | hoverPen=hover_pen, 565 | handlePen=handle_pen, 566 | handleHoverPen=hover_handle, 567 | movable=False, 568 | ) 569 | self.diffraction_space_widget.getView().addItem(self.virtual_detector_roi_inner) 570 | 571 | # Connect size/position of inner and outer detectors 572 | self.virtual_detector_roi_outer.sigRegionChanged.connect( 573 | self.update_annulus_pos 574 | ) 575 | self.virtual_detector_roi_outer.sigRegionChanged.connect( 576 | self.update_annulus_radii 577 | ) 578 | self.virtual_detector_roi_inner.sigRegionChanged.connect( 579 | self.update_annulus_radii 580 | ) 581 | 582 | # Connect to real space view update function 583 | self.virtual_detector_roi_outer.sigRegionChangeFinished.connect( 584 | partial(self.update_real_space_view, False) 585 | ) 586 | self.virtual_detector_roi_inner.sigRegionChangeFinished.connect( 587 | partial(self.update_real_space_view, False) 588 | ) 589 | 590 | else: 591 | raise ValueError("Unknown detector shape! Got: {}".format(detector_shape)) 592 | 593 | self.update_real_space_view(reset=True) 594 | 595 | 596 | def set_diffraction_autoscale_range(self, percentiles, redraw=True): 597 | self.diffraction_autoscale_percentiles = percentiles 598 | self.settings.setValue("last_state/diffraction_autorange", list(percentiles)) 599 | 600 | if redraw: 601 | self._render_diffraction_image(reset=False) 602 | 603 | 604 | def set_real_space_autoscale_range(self, percentiles, redraw=True): 605 | self.real_space_autoscale_percentiles = percentiles 606 | self.settings.setValue("last_state/realspace_autorange", list(percentiles)) 607 | 608 | if redraw: 609 | self._render_virtual_image(reset=False) 610 | 611 | 612 | def nudge_real_space_selector(self, dx, dy): 613 | if ( 614 | hasattr(self, "real_space_point_selector") 615 | and self.real_space_point_selector is not None 616 | ): 617 | selector = self.real_space_point_selector 618 | elif ( 619 | hasattr(self, "real_space_rect_selector") 620 | and self.real_space_rect_selector is not None 621 | ): 622 | selector = self.real_space_rect_selector 623 | else: 624 | raise RuntimeError("Can't find the real space selector!") 625 | 626 | position = selector.pos() 627 | position[0] += dy 628 | position[1] += dx 629 | 630 | selector.setPos(position) 631 | 632 | 633 | def nudge_diffraction_selector(self, dx, dy): 634 | if ( 635 | hasattr(self, "virtual_detector_point") 636 | and self.virtual_detector_point is not None 637 | ): 638 | selector = self.virtual_detector_point 639 | elif ( 640 | hasattr(self, "virtual_detector_roi") and self.virtual_detector_roi is not None 641 | ): 642 | selector = self.virtual_detector_roi 643 | elif ( 644 | hasattr(self, "virtual_detector_roi_outer") 645 | and self.virtual_detector_roi_outer is not None 646 | ): 647 | selector = self.virtual_detector_roi_outer 648 | else: 649 | raise RuntimeError("Can't find the diffraction space selector!") 650 | 651 | position = selector.pos() 652 | position[0] += dy 653 | position[1] += dx 654 | 655 | selector.setPos(position) 656 | 657 | 658 | def update_tooltip(self): 659 | modifier_keys = QApplication.queryKeyboardModifiers() 660 | 661 | if self.datacube is not None and self.isActiveWindow(): 662 | global_pos = QCursor.pos() 663 | 664 | for scene, data in [ 665 | (self.diffraction_space_widget, self.unscaled_diffraction_image), 666 | (self.real_space_widget, self.unscaled_realspace_image), 667 | (self.fft_widget, self.unscaled_fft_image), 668 | ]: 669 | pos_in_scene = scene.mapFromGlobal(QCursor.pos()) 670 | if scene.getView().rect().contains(pos_in_scene): 671 | pos_in_data = scene.view.mapSceneToView(pos_in_scene) 672 | 673 | y = int(np.clip(np.floor(pos_in_data.x()), 0, data.shape[1] - 1)) 674 | x = int(np.clip(np.floor(pos_in_data.y()), 0, data.shape[0] - 1)) 675 | 676 | if np.isrealobj(data): 677 | display_text = f"[{x},{y}]: {data[x,y]:.5g}" 678 | else: 679 | display_text = f"[{x},{y}]: |z|={np.abs(data[x,y]):.5g}, ϕ={np.degrees(np.angle(data[x,y])):.5g}°" 680 | 681 | self.cursor_value_text.setText(display_text) 682 | 683 | 684 | def update_annulus_pos(self): 685 | """ 686 | Function to keep inner and outer rings of annulus aligned. 687 | """ 688 | R_outer = self.virtual_detector_roi_outer.size().x() / 2 689 | R_inner = self.virtual_detector_roi_inner.size().x() / 2 690 | # Only outer annulus is draggable; when it moves, update position of inner annulus 691 | x0 = self.virtual_detector_roi_outer.pos().x() + R_outer 692 | y0 = self.virtual_detector_roi_outer.pos().y() + R_outer 693 | self.virtual_detector_roi_inner.setPos(x0 - R_inner, y0 - R_inner, update=False) 694 | 695 | 696 | def update_annulus_radii(self): 697 | R_outer = self.virtual_detector_roi_outer.size().x() / 2 698 | R_inner = self.virtual_detector_roi_inner.size().x() / 2 699 | if R_outer < R_inner: 700 | x0 = self.virtual_detector_roi_outer.pos().x() + R_outer 701 | y0 = self.virtual_detector_roi_outer.pos().y() + R_outer 702 | self.virtual_detector_roi_outer.setSize(2 * R_inner + 6, update=False) 703 | self.virtual_detector_roi_outer.setPos( 704 | x0 - R_inner - 3, y0 - R_inner - 3, update=False 705 | ) 706 | -------------------------------------------------------------------------------- /src/py4D_browser/utils.py: -------------------------------------------------------------------------------- 1 | import pyqtgraph as pg 2 | import numpy as np 3 | from PyQt5.QtWidgets import QFrame, QPushButton, QApplication, QLabel 4 | from PyQt5.QtCore import pyqtSignal 5 | from PyQt5.QtCore import Qt, QObject 6 | from PyQt5.QtWidgets import QDialog, QHBoxLayout, QVBoxLayout, QSpinBox 7 | 8 | 9 | class StatusBarWriter: 10 | def __init__(self, statusBar): 11 | self.statusBar = statusBar 12 | self.app = app = QApplication.instance() 13 | 14 | def write(self, message): 15 | self.statusBar.showMessage(message, 1_000) 16 | self.app.processEvents() 17 | 18 | def flush(self): 19 | pass 20 | 21 | 22 | class VLine(QFrame): 23 | # a simple vertical divider line 24 | def __init__(self): 25 | super(VLine, self).__init__() 26 | self.setFrameShape(self.VLine | self.Sunken) 27 | 28 | 29 | class LatchingButton(QPushButton): 30 | """ 31 | Subclass of QPushButton that acts as a momentary button, 32 | unless shift is held down during the click, in which case 33 | it toggles on. 34 | Emits the "activated" signal whenever triggered, and 35 | maintains the "latched" state when latched down. 36 | """ 37 | 38 | activated = pyqtSignal() 39 | 40 | def __init__(self, *args, **kwargs): 41 | self.status_bar = kwargs.pop("status_bar", None) 42 | self.latched = kwargs.pop("latched", False) 43 | super().__init__(*args, **kwargs) 44 | self.setCheckable(True) 45 | self.clicked.connect(self.on_click) 46 | if self.latched: 47 | self.setChecked(True) 48 | self.activated.emit() 49 | 50 | def on_click(self, *args): 51 | modifiers = QApplication.keyboardModifiers() 52 | 53 | if self.latched: 54 | self.setChecked(False) 55 | self.latched = False 56 | else: 57 | if modifiers == Qt.ShiftModifier: 58 | self.setChecked(True) 59 | self.latched = True 60 | self.activated.emit() 61 | else: 62 | self.setChecked(False) 63 | self.latched = False 64 | self.activated.emit() 65 | if self.status_bar is not None: 66 | self.status_bar.showMessage("Shift+click to keep on", 5_000) 67 | 68 | 69 | def pg_point_roi(view_box, center=(-0.5, -0.5), pen=(0, 9), hoverPen=None): 70 | """ 71 | Point selection. Based in pyqtgraph, and returns a pyqtgraph CircleROI object. 72 | This object has a sigRegionChanged.connect() signal method to connect to other functions. 73 | """ 74 | circ_roi = pg.CircleROI(center, (2, 2), movable=True, pen=pen, hoverPen=hoverPen) 75 | h = circ_roi.addTranslateHandle((0.5, 0.5)) 76 | h.pen = pg.mkPen("r") 77 | h.update() 78 | view_box.addItem(circ_roi) 79 | circ_roi.removeHandle(0) 80 | return circ_roi 81 | 82 | 83 | def make_detector(shape: tuple, mode: str, geometry) -> np.ndarray: 84 | match mode, geometry: 85 | case ["point", (qx, qy)]: 86 | mask = np.zeros(shape, dtype=np.bool_) 87 | mask[qx, qy] = True 88 | case ["point", geom]: 89 | raise ValueError( 90 | f"Point detector shape must be specified as (qx,qy), not {geom}" 91 | ) 92 | 93 | case [("circle" | "circular"), ((qx, qy), r)]: 94 | ix, iy = np.indices(shape) 95 | mask = np.hypot(ix - qx, iy - qy) <= r 96 | case [("circle" | "circular"), geom]: 97 | raise ValueError( 98 | f"Circular detector shape must be specified as ((qx,qy),r), not {geom}" 99 | ) 100 | 101 | case [("annulus" | "annular"), ((qx, qy), (ri, ro))]: 102 | ix, iy = np.indices(shape) 103 | ir = np.hypot(ix - qx, iy - qy) 104 | mask = np.logical_and(ir >= ri, ir <= ro) 105 | case [("annulus" | "annular"), geom]: 106 | raise ValueError( 107 | f"Annular detector shape must be specified as ((qx,qy),(ri,ro)), not {geom}" 108 | ) 109 | 110 | case [("rectangle" | "square" | "rectangular"), (xmin, xmax, ymin, ymax)]: 111 | mask = np.zeros(shape, dtype=np.bool_) 112 | mask[xmin:xmax, ymin:ymax] = True 113 | case [("rectangle" | "square" | "rectangular"), geom]: 114 | raise ValueError( 115 | f"Rectangular detector shape must be specified as (xmin,xmax,ymin,ymax), not {geom}" 116 | ) 117 | 118 | case ["mask", mask_arr]: 119 | mask = mask_arr 120 | 121 | case unknown: 122 | raise ValueError(f"mode and geometry not understood: {unknown}") 123 | 124 | return mask 125 | 126 | 127 | def complex_to_Lab( 128 | im, amin=None, amax=None, gamma=1.0, L_scale=100, ab_scale=64, uniform_L=None 129 | ): 130 | from skimage.color import lab2rgb 131 | from matplotlib.colors import Normalize 132 | import warnings 133 | 134 | Lab = np.zeros(im.shape + (3,), dtype=np.float64) 135 | angle = np.angle(im) 136 | 137 | L = Normalize(vmin=amin, vmax=amax, clip=True)(np.abs(im)) ** gamma 138 | L = Normalize()(L) 139 | 140 | # attempt at polynomial saturation 141 | # ab_prescale = 4*L - 4*L*L 142 | ab_prescale = 0.5 143 | 144 | Lab[..., 0] = uniform_L or L * L_scale 145 | Lab[..., 1] = np.cos(angle) * ab_scale * ab_prescale 146 | Lab[..., 2] = np.sin(angle) * ab_scale * ab_prescale 147 | 148 | with warnings.catch_warnings(): 149 | warnings.simplefilter("ignore") 150 | rgb = lab2rgb(Lab) 151 | 152 | return rgb 153 | --------------------------------------------------------------------------------