├── .github └── workflows │ └── python-package.yml ├── .readthedocs.yaml ├── CITATION.cff ├── CONTRIBUTING.rst ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── build │ ├── docs │ │ └── _static │ │ │ ├── _sphinx_javascript_frameworks_compat.js │ │ │ └── jquery.js │ ├── doctrees │ │ ├── _templates │ │ │ └── autosummary │ │ │ │ └── class.doctree │ │ ├── analysis.doctree │ │ ├── auto_examples │ │ │ ├── index.doctree │ │ │ ├── plot_i_package_overview.doctree │ │ │ ├── plot_i_preprocessing_pipelines.doctree │ │ │ ├── plot_ii_dl_denoising.doctree │ │ │ ├── plot_iii_bacteria_classification.doctree │ │ │ └── sg_execution_times.doctree │ │ ├── auto_tutorials │ │ │ ├── i-classes │ │ │ │ ├── plot_i_generic_container.doctree │ │ │ │ ├── plot_ii_spectrum_container.doctree │ │ │ │ ├── plot_iii_image_container.doctree │ │ │ │ ├── plot_iv_volume_container.doctree │ │ │ │ └── sg_execution_times.doctree │ │ │ ├── ii-instrumental │ │ │ │ ├── i_witec.doctree │ │ │ │ ├── ii_renishaw.doctree │ │ │ │ ├── iii_ocean_insight.doctree │ │ │ │ └── iv_other.doctree │ │ │ ├── iii-datasets │ │ │ │ ├── ii_rruff.doctree │ │ │ │ ├── plot_i_bacteria.doctree │ │ │ │ ├── plot_ii_metrics.doctree │ │ │ │ └── sg_execution_times.doctree │ │ │ ├── index.doctree │ │ │ ├── iv-viz │ │ │ │ ├── plot_i_spectra.doctree │ │ │ │ ├── plot_ii_mean_spectra.doctree │ │ │ │ ├── plot_ii_peaks.doctree │ │ │ │ ├── plot_ii_spectra_mean.doctree │ │ │ │ ├── plot_iii_image.doctree │ │ │ │ ├── plot_iv_volume.doctree │ │ │ │ ├── plot_v_peak_dist.doctree │ │ │ │ ├── plot_vi_customisation.doctree │ │ │ │ └── sg_execution_times.doctree │ │ │ ├── v-preprocessing │ │ │ │ ├── plot_i_predefined_methods.doctree │ │ │ │ ├── plot_ii_custom_method.doctree │ │ │ │ ├── plot_iii_custom_pipeline.doctree │ │ │ │ ├── plot_iv_predefined_pipeline.doctree │ │ │ │ └── sg_execution_times.doctree │ │ │ ├── vi-analysis │ │ │ │ ├── plot_i_decomposition.doctree │ │ │ │ ├── plot_ii_kmeans.doctree │ │ │ │ ├── plot_iii_unmixing.doctree │ │ │ │ ├── plot_iv_integrative_svm.doctree │ │ │ │ ├── plot_v_integrative_nn.doctree │ │ │ │ └── sg_execution_times.doctree │ │ │ └── vii-synth │ │ │ │ ├── plot_i_endmembers.doctree │ │ │ │ └── sg_execution_times.doctree │ │ ├── data_classes.doctree │ │ ├── datasets.doctree │ │ ├── environment.pickle │ │ ├── examples │ │ │ └── README.doctree │ │ ├── generated │ │ │ ├── analysis │ │ │ │ ├── cluster │ │ │ │ │ └── ramanspy.analysis.cluster.KMeans.doctree │ │ │ │ ├── decompose │ │ │ │ │ ├── ramanspy.analysis.decompose.ICA.doctree │ │ │ │ │ ├── ramanspy.analysis.decompose.NMF.doctree │ │ │ │ │ └── ramanspy.analysis.decompose.PCA.doctree │ │ │ │ └── unmix │ │ │ │ │ ├── ramanspy.analysis.unmix.FIPPI.doctree │ │ │ │ │ ├── ramanspy.analysis.unmix.NFINDR.doctree │ │ │ │ │ ├── ramanspy.analysis.unmix.PPI.doctree │ │ │ │ │ └── ramanspy.analysis.unmix.VCA.doctree │ │ │ └── prepprocessing │ │ │ │ ├── baseline │ │ │ │ ├── ramanspy.preprocessing.baseline.AIRPLS.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.ARPLS.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.ASLS.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.ASPLS.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.CornerCutting.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.DRPLS.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.FABC.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.Goldindec.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.IARPLS.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.IASLS.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.IRSQR.doctree │ │ │ │ ├── ramanspy.preprocessing.baseline.ModPoly.doctree │ │ │ │ └── ramanspy.preprocessing.baseline.Poly.doctree │ │ │ │ ├── denoising │ │ │ │ ├── ramanspy.preprocessing.denoise.Gaussian.doctree │ │ │ │ ├── ramanspy.preprocessing.denoise.Kernel.doctree │ │ │ │ ├── ramanspy.preprocessing.denoise.SavGol.doctree │ │ │ │ └── ramanspy.preprocessing.denoise.Whittaker.doctree │ │ │ │ ├── despiking │ │ │ │ └── ramanspy.preprocessing.despike.WhitakerHayes.doctree │ │ │ │ ├── misc │ │ │ │ ├── ramanspy.preprocessing.misc.BackgroundSubtractor.doctree │ │ │ │ └── ramanspy.preprocessing.misc.Cropper.doctree │ │ │ │ ├── norm │ │ │ │ ├── ramanspy.preprocessing.normalise.AUC.doctree │ │ │ │ ├── ramanspy.preprocessing.normalise.MaxIntensity.doctree │ │ │ │ ├── ramanspy.preprocessing.normalise.MinMax.doctree │ │ │ │ └── ramanspy.preprocessing.normalise.Vector.doctree │ │ │ │ └── protocols │ │ │ │ ├── ramanspy.preprocessing.protocols.bergholt2016.doctree │ │ │ │ ├── ramanspy.preprocessing.protocols.georgiev2023_P1.doctree │ │ │ │ └── ramanspy.preprocessing.protocols.georgiev2023_P3.doctree │ │ ├── index.doctree │ │ ├── installation.doctree │ │ ├── loading.doctree │ │ ├── metrics.doctree │ │ ├── overview.doctree │ │ ├── plot.doctree │ │ ├── preprocessing.doctree │ │ ├── synth.doctree │ │ ├── tutorials │ │ │ ├── README.doctree │ │ │ ├── i-classes │ │ │ │ └── README.doctree │ │ │ ├── ii-instrumental │ │ │ │ └── README.doctree │ │ │ ├── iii-datasets │ │ │ │ ├── -README.doctree │ │ │ │ └── README.doctree │ │ │ ├── iv-viz │ │ │ │ └── README.doctree │ │ │ ├── v-preprocessing │ │ │ │ └── README.doctree │ │ │ ├── vi-analysis │ │ │ │ └── README.doctree │ │ │ └── vii-synth │ │ │ │ └── README.doctree │ │ └── viz.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _downloads │ │ ├── 06a4d1c020efd332289ceb99707f981f │ │ │ └── plot_i_decomposition.ipynb │ │ ├── 07fcc19ba03226cd3d83d4e40ec44385 │ │ │ └── auto_examples_python.zip │ │ ├── 0b030be7b180617d677dd81fe92b413e │ │ │ └── plot_ii_spectra_mean.ipynb │ │ ├── 0eef8b3a78a6c41f20da229f36d285f6 │ │ │ └── plot_iv_integrative_svm.ipynb │ │ ├── 121817dffc37085e7cba37be361ab8fb │ │ │ └── plot_ii_kmeans.ipynb │ │ ├── 1404a83df5094668a673349fef8ec679 │ │ │ └── plot_vi_customisation.ipynb │ │ ├── 148e7a9ddb0bd31b193a6d294612c3d4 │ │ │ └── i_witec.py │ │ ├── 1928db286fef5330a95492f4263b9b64 │ │ │ └── plot_iii_image_container.ipynb │ │ ├── 1b3a8cd44cecaae6ba900a04bff6b2e7 │ │ │ └── iv_other.ipynb │ │ ├── 1cb459dea7c9d01ee90118353dc880f0 │ │ │ └── plot_i_decomposition.py │ │ ├── 208ea2ce3d891e0316a8fb17d9fe77f2 │ │ │ └── plot_i_endmembers.ipynb │ │ ├── 28b6e3a8d88ed094fb515929ea899e4b │ │ │ └── plot_iv_volume.py │ │ ├── 2a70b0fb2b899cec8dd0e878a320430d │ │ │ └── plot_i_bacteria.ipynb │ │ ├── 2af6c0be6ed6043e491fbb8d173116f8 │ │ │ └── plot_iv_predefined_pipeline.py │ │ ├── 2c0b96688155d93047f369fe6b6b2910 │ │ │ └── plot_iii_image.py │ │ ├── 2fa9503ee3eb4470dd13b3e10acedd9d │ │ │ └── iv_other.py │ │ ├── 39b0c902ea783b0d6925af48841e8c56 │ │ │ └── plot_ii_kmeans.py │ │ ├── 3d24e1d5d22d6b3d55335c090eadb4ef │ │ │ └── plot_iv_volume_container.py │ │ ├── 3e38db876fbbbfbf7bf4d5973c9f9de2 │ │ │ └── plot_ii_spectrum_container.py │ │ ├── 41656651d1b6b62c42a6835280ee481c │ │ │ └── plot_iii_custom_pipeline.py │ │ ├── 424adee97e9931653877ffef0b55d031 │ │ │ └── plot_i_generic_container.py │ │ ├── 43ac4abf1e577d3e73c7ebfa5dbd9345 │ │ │ └── i_witec.ipynb │ │ ├── 48ae910b0b2517b77af0177756aa2bea │ │ │ └── iii_ocean_insight.py │ │ ├── 50c99b749c9f0fff2d20e213a4cf14de │ │ │ └── plot_i_spectra.ipynb │ │ ├── 51e7ca26ad674053cc1d3ebdce348e09 │ │ │ └── plot_ii_peaks.ipynb │ │ ├── 52073867785117c31fe34b88eba3f264 │ │ │ └── plot_i_predefined_methods.ipynb │ │ ├── 52676b36d1bcfb10b6d5233b0e3f4740 │ │ │ └── plot_ii_metrics.ipynb │ │ ├── 55af60f9b2020db5b2ecf72ea7bde4c3 │ │ │ └── plot_iii_unmixing.py │ │ ├── 5a6709622ae43d3c4d45712479480c57 │ │ │ └── plot_ii_custom_method.py │ │ ├── 61677e5462defd3fd4c468950867ac1e │ │ │ └── plot_ii_custom_method.ipynb │ │ ├── 62c839415c8123b21a0f26d8b918729d │ │ │ └── ii_renishaw.ipynb │ │ ├── 6325a124ac282dd33f881d8053b3e9bf │ │ │ └── plot_vi_customisation.py │ │ ├── 63c7d1e5884a56af3102289709179bb1 │ │ │ └── plot_ii_dl_denoising.py │ │ ├── 66401b96967d564294e231eb47edf226 │ │ │ └── plot_v_peak_dist.py │ │ ├── 670fd95bf21e1c4dd904595909b41983 │ │ │ └── plot_ii_spectra_mean.py │ │ ├── 6c511c6608f6224990b08eb81f303005 │ │ │ └── plot_iii_image_container.py │ │ ├── 6f1e7a639e0699d6164445b55e6c116d │ │ │ └── auto_examples_jupyter.zip │ │ ├── 70e10bd041d70ec300139bffe622890f │ │ │ └── plot_i_preprocessing_pipelines.ipynb │ │ ├── 72c1f4c74f8fb530820294ff5d0f143f │ │ │ └── plot_v_integrative_nn.py │ │ ├── 74d07ad730e72df7af2ce191ac5df6ce │ │ │ └── plot_iii_unmixing.ipynb │ │ ├── 7b8fbe32fb15db2865867f06aebc31e1 │ │ │ └── plot_i_endmembers.py │ │ ├── 7e847fa9034ec44113f9bd8522c79683 │ │ │ └── plot_ii_mean_spectra.py │ │ ├── 8a980b1ab860429370b804cb7c326bb4 │ │ │ └── plot_iv_volume.ipynb │ │ ├── 97a1de59bce682890841bb846e3dd09c │ │ │ └── auto_tutorials_jupyter.zip │ │ ├── 9c02060426e38e0c8e9d538c1bb657c7 │ │ │ └── plot_i_preprocessing_pipelines.py │ │ ├── 9da78011b06d1bdb69867f4b9ae05b9e │ │ │ └── plot_ii_spectrum_container.ipynb │ │ ├── 9dd846619c712411a95b44a7486d740f │ │ │ └── ii_rruff.ipynb │ │ ├── a01a44409a93be3c5a290a9eec74d4ad │ │ │ └── plot_i_package_overview.py │ │ ├── a1a8b269f4f7c0f6a0aa6e68c3a2c672 │ │ │ └── plot_ii_mean_spectra.ipynb │ │ ├── a40b220e44a205192729aa41ece5110c │ │ │ └── plot_ii_metrics.py │ │ ├── a59a8a43ccbfebaaf5e8c98828078831 │ │ │ └── ii_rruff.py │ │ ├── aabed4cfc78f0f3fc1944ade670c0f94 │ │ │ └── plot_i_bacteria.py │ │ ├── b10659896e45369c4e0796bd26a6d3d0 │ │ │ └── plot_iii_bacteria_classification.py │ │ ├── b130d8cc5afa844a39b06bf8366ec619 │ │ │ └── plot_iii_image.ipynb │ │ ├── b5691425122ad036bc6502e2dc989186 │ │ │ └── plot_iv_volume_container.ipynb │ │ ├── c3eafda35b3aa4abd990d48fefd4d558 │ │ │ └── plot_v_integrative_nn.ipynb │ │ ├── cab7a090c4183ca69dc0cd84d3b04413 │ │ │ └── auto_tutorials_python.zip │ │ ├── cd1b15cae80fcdf13744ad6dc2110d7b │ │ │ └── plot_i_generic_container.ipynb │ │ ├── d82e73c01b6c50095b1b356c6c47e8a4 │ │ │ └── plot_ii_dl_denoising.ipynb │ │ ├── d94bbd58d69bf52dd2253d3d1df352cf │ │ │ └── iii_ocean_insight.ipynb │ │ ├── d9f43a311a24bb163b2bc2df1f242fd8 │ │ │ └── plot_iii_bacteria_classification.ipynb │ │ ├── dba8396cb1ad2377aecb47912d26bf68 │ │ │ └── plot_iv_integrative_svm.py │ │ ├── e4aa1894780cad83e2769db18ef0b839 │ │ │ └── plot_iii_custom_pipeline.ipynb │ │ ├── e8a7617b87571d33b8c07f858aced1a0 │ │ │ └── plot_i_predefined_methods.py │ │ ├── f108ddc966014e1f6d9a63597272d785 │ │ │ └── plot_i_package_overview.ipynb │ │ ├── f120bef3d275e7b25516e8bfc1ace949 │ │ │ └── plot_ii_peaks.py │ │ ├── f13f5a83df8fe4e2f71f675f7970cd63 │ │ │ └── ii_renishaw.py │ │ ├── f3534999af9b5b42d4bb210c83ef11bd │ │ │ └── plot_i_spectra.py │ │ ├── fdf9172f6e1f349712607758dbc3ca35 │ │ │ └── plot_iv_predefined_pipeline.ipynb │ │ └── ff8c4da9032d200d102e1da05a80bd8e │ │ │ └── plot_v_peak_dist.ipynb │ │ ├── _images │ │ ├── package_overview__.png │ │ ├── sphx_glr_i_witec_thumb.png │ │ ├── sphx_glr_ii_renishaw_thumb.png │ │ ├── sphx_glr_ii_rruff_thumb.png │ │ ├── sphx_glr_iii_ocean_insight_thumb.png │ │ ├── sphx_glr_iv_other_thumb.png │ │ ├── sphx_glr_plot_i_bacteria_001.png │ │ ├── sphx_glr_plot_i_bacteria_thumb.png │ │ ├── sphx_glr_plot_i_decomposition_001.png │ │ ├── sphx_glr_plot_i_decomposition_002.png │ │ ├── sphx_glr_plot_i_decomposition_003.png │ │ ├── sphx_glr_plot_i_decomposition_004.png │ │ ├── sphx_glr_plot_i_decomposition_005.png │ │ ├── sphx_glr_plot_i_decomposition_006.png │ │ ├── sphx_glr_plot_i_decomposition_007.png │ │ ├── sphx_glr_plot_i_decomposition_008.png │ │ ├── sphx_glr_plot_i_decomposition_009.png │ │ ├── sphx_glr_plot_i_decomposition_thumb.png │ │ ├── sphx_glr_plot_i_endmembers_001.png │ │ ├── sphx_glr_plot_i_endmembers_thumb.png │ │ ├── sphx_glr_plot_i_generic_container_001.png │ │ ├── sphx_glr_plot_i_generic_container_thumb.png │ │ ├── sphx_glr_plot_i_package_overview_001.png │ │ ├── sphx_glr_plot_i_package_overview_002.png │ │ ├── sphx_glr_plot_i_package_overview_003.png │ │ ├── sphx_glr_plot_i_package_overview_004.png │ │ ├── sphx_glr_plot_i_package_overview_005.png │ │ ├── sphx_glr_plot_i_package_overview_006.png │ │ ├── sphx_glr_plot_i_package_overview_007.png │ │ ├── sphx_glr_plot_i_package_overview_008.png │ │ ├── sphx_glr_plot_i_package_overview_009.png │ │ ├── sphx_glr_plot_i_package_overview_010.png │ │ ├── sphx_glr_plot_i_package_overview_011.png │ │ ├── sphx_glr_plot_i_package_overview_012.png │ │ ├── sphx_glr_plot_i_package_overview_013.png │ │ ├── sphx_glr_plot_i_package_overview_014.png │ │ ├── sphx_glr_plot_i_package_overview_015.png │ │ ├── sphx_glr_plot_i_package_overview_016.png │ │ ├── sphx_glr_plot_i_package_overview_017.png │ │ ├── sphx_glr_plot_i_package_overview_018.png │ │ ├── sphx_glr_plot_i_package_overview_019.png │ │ ├── sphx_glr_plot_i_package_overview_020.png │ │ ├── sphx_glr_plot_i_package_overview_021.png │ │ ├── sphx_glr_plot_i_package_overview_022.png │ │ ├── sphx_glr_plot_i_package_overview_023.png │ │ ├── sphx_glr_plot_i_package_overview_thumb.png │ │ ├── sphx_glr_plot_i_predefined_methods_001.png │ │ ├── sphx_glr_plot_i_predefined_methods_002.png │ │ ├── sphx_glr_plot_i_predefined_methods_003.png │ │ ├── sphx_glr_plot_i_predefined_methods_004.png │ │ ├── sphx_glr_plot_i_predefined_methods_005.png │ │ ├── sphx_glr_plot_i_predefined_methods_006.png │ │ ├── sphx_glr_plot_i_predefined_methods_thumb.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_001.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_002.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_003.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_004.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_005.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_006.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_007.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_008.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_009.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_010.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_thumb.png │ │ ├── sphx_glr_plot_i_spectra_001.png │ │ ├── sphx_glr_plot_i_spectra_002.png │ │ ├── sphx_glr_plot_i_spectra_003.png │ │ ├── sphx_glr_plot_i_spectra_004.png │ │ ├── sphx_glr_plot_i_spectra_005.png │ │ ├── sphx_glr_plot_i_spectra_006.png │ │ ├── sphx_glr_plot_i_spectra_007.png │ │ ├── sphx_glr_plot_i_spectra_008.png │ │ ├── sphx_glr_plot_i_spectra_009.png │ │ ├── sphx_glr_plot_i_spectra_010.png │ │ ├── sphx_glr_plot_i_spectra_011.png │ │ ├── sphx_glr_plot_i_spectra_012.png │ │ ├── sphx_glr_plot_i_spectra_013.png │ │ ├── sphx_glr_plot_i_spectra_014.png │ │ ├── sphx_glr_plot_i_spectra_015.png │ │ ├── sphx_glr_plot_i_spectra_thumb.png │ │ ├── sphx_glr_plot_ii_custom_method_001.png │ │ ├── sphx_glr_plot_ii_custom_method_002.png │ │ ├── sphx_glr_plot_ii_custom_method_003.png │ │ ├── sphx_glr_plot_ii_custom_method_thumb.png │ │ ├── sphx_glr_plot_ii_dl_denoising_001.png │ │ ├── sphx_glr_plot_ii_dl_denoising_002.png │ │ ├── sphx_glr_plot_ii_dl_denoising_003.png │ │ ├── sphx_glr_plot_ii_dl_denoising_004.png │ │ ├── sphx_glr_plot_ii_dl_denoising_005.png │ │ ├── sphx_glr_plot_ii_dl_denoising_006.png │ │ ├── sphx_glr_plot_ii_dl_denoising_007.png │ │ ├── sphx_glr_plot_ii_dl_denoising_008.png │ │ ├── sphx_glr_plot_ii_dl_denoising_thumb.png │ │ ├── sphx_glr_plot_ii_kmeans_001.png │ │ ├── sphx_glr_plot_ii_kmeans_002.png │ │ ├── sphx_glr_plot_ii_kmeans_003.png │ │ ├── sphx_glr_plot_ii_kmeans_004.png │ │ ├── sphx_glr_plot_ii_kmeans_005.png │ │ ├── sphx_glr_plot_ii_kmeans_006.png │ │ ├── sphx_glr_plot_ii_kmeans_thumb.png │ │ ├── sphx_glr_plot_ii_mean_spectra_001.png │ │ ├── sphx_glr_plot_ii_mean_spectra_002.png │ │ ├── sphx_glr_plot_ii_mean_spectra_003.png │ │ ├── sphx_glr_plot_ii_mean_spectra_004.png │ │ ├── sphx_glr_plot_ii_mean_spectra_005.png │ │ ├── sphx_glr_plot_ii_mean_spectra_006.png │ │ ├── sphx_glr_plot_ii_mean_spectra_007.png │ │ ├── sphx_glr_plot_ii_mean_spectra_008.png │ │ ├── sphx_glr_plot_ii_mean_spectra_009.png │ │ ├── sphx_glr_plot_ii_metrics_001.png │ │ ├── sphx_glr_plot_ii_metrics_thumb.png │ │ ├── sphx_glr_plot_ii_peaks_001.png │ │ ├── sphx_glr_plot_ii_peaks_thumb.png │ │ ├── sphx_glr_plot_ii_spectra_mean_001.png │ │ ├── sphx_glr_plot_ii_spectra_mean_002.png │ │ ├── sphx_glr_plot_ii_spectra_mean_003.png │ │ ├── sphx_glr_plot_ii_spectra_mean_004.png │ │ ├── sphx_glr_plot_ii_spectra_mean_005.png │ │ ├── sphx_glr_plot_ii_spectra_mean_006.png │ │ ├── sphx_glr_plot_ii_spectra_mean_007.png │ │ ├── sphx_glr_plot_ii_spectra_mean_008.png │ │ ├── sphx_glr_plot_ii_spectra_mean_009.png │ │ ├── sphx_glr_plot_ii_spectra_mean_thumb.png │ │ ├── sphx_glr_plot_ii_spectrum_container_001.png │ │ ├── sphx_glr_plot_ii_spectrum_container_thumb.png │ │ ├── sphx_glr_plot_iii_bacteria_classification_001.png │ │ ├── sphx_glr_plot_iii_bacteria_classification_002.png │ │ ├── sphx_glr_plot_iii_bacteria_classification_003.png │ │ ├── sphx_glr_plot_iii_bacteria_classification_004.png │ │ ├── sphx_glr_plot_iii_bacteria_classification_thumb.png │ │ ├── sphx_glr_plot_iii_custom_pipeline_001.png │ │ ├── sphx_glr_plot_iii_custom_pipeline_002.png │ │ ├── sphx_glr_plot_iii_custom_pipeline_003.png │ │ ├── sphx_glr_plot_iii_custom_pipeline_004.png │ │ ├── sphx_glr_plot_iii_custom_pipeline_005.png │ │ ├── sphx_glr_plot_iii_custom_pipeline_006.png │ │ ├── sphx_glr_plot_iii_custom_pipeline_thumb.png │ │ ├── sphx_glr_plot_iii_image_001.png │ │ ├── sphx_glr_plot_iii_image_002.png │ │ ├── sphx_glr_plot_iii_image_003.png │ │ ├── sphx_glr_plot_iii_image_004.png │ │ ├── sphx_glr_plot_iii_image_005.png │ │ ├── sphx_glr_plot_iii_image_006.png │ │ ├── sphx_glr_plot_iii_image_container_001.png │ │ ├── sphx_glr_plot_iii_image_container_002.png │ │ ├── sphx_glr_plot_iii_image_container_003.png │ │ ├── sphx_glr_plot_iii_image_container_thumb.png │ │ ├── sphx_glr_plot_iii_image_thumb.png │ │ ├── sphx_glr_plot_iii_unmixing_001.png │ │ ├── sphx_glr_plot_iii_unmixing_002.png │ │ ├── sphx_glr_plot_iii_unmixing_003.png │ │ ├── sphx_glr_plot_iii_unmixing_004.png │ │ ├── sphx_glr_plot_iii_unmixing_005.png │ │ ├── sphx_glr_plot_iii_unmixing_006.png │ │ ├── sphx_glr_plot_iii_unmixing_007.png │ │ ├── sphx_glr_plot_iii_unmixing_008.png │ │ ├── sphx_glr_plot_iii_unmixing_009.png │ │ ├── sphx_glr_plot_iii_unmixing_thumb.png │ │ ├── sphx_glr_plot_iv_integrative_svm_001.png │ │ ├── sphx_glr_plot_iv_integrative_svm_thumb.png │ │ ├── sphx_glr_plot_iv_predefined_pipeline_001.png │ │ ├── sphx_glr_plot_iv_predefined_pipeline_002.png │ │ ├── sphx_glr_plot_iv_predefined_pipeline_thumb.png │ │ ├── sphx_glr_plot_iv_volume_001.png │ │ ├── sphx_glr_plot_iv_volume_002.png │ │ ├── sphx_glr_plot_iv_volume_003.png │ │ ├── sphx_glr_plot_iv_volume_004.png │ │ ├── sphx_glr_plot_iv_volume_container_001.png │ │ ├── sphx_glr_plot_iv_volume_container_002.png │ │ ├── sphx_glr_plot_iv_volume_container_003.png │ │ ├── sphx_glr_plot_iv_volume_container_thumb.png │ │ ├── sphx_glr_plot_iv_volume_thumb.png │ │ ├── sphx_glr_plot_v_integrative_nn_001.png │ │ ├── sphx_glr_plot_v_integrative_nn_002.png │ │ ├── sphx_glr_plot_v_integrative_nn_003.png │ │ ├── sphx_glr_plot_v_integrative_nn_thumb.png │ │ ├── sphx_glr_plot_v_peak_dist_001.png │ │ ├── sphx_glr_plot_v_peak_dist_002.png │ │ ├── sphx_glr_plot_v_peak_dist_003.png │ │ ├── sphx_glr_plot_v_peak_dist_004.png │ │ ├── sphx_glr_plot_v_peak_dist_005.png │ │ ├── sphx_glr_plot_v_peak_dist_thumb.png │ │ ├── sphx_glr_plot_vi_customisation_001.png │ │ ├── sphx_glr_plot_vi_customisation_002.png │ │ ├── sphx_glr_plot_vi_customisation_003.png │ │ ├── sphx_glr_plot_vi_customisation_004.png │ │ ├── sphx_glr_plot_vi_customisation_005.png │ │ ├── sphx_glr_plot_vi_customisation_006.png │ │ ├── sphx_glr_plot_vi_customisation_007.png │ │ ├── sphx_glr_plot_vi_customisation_008.png │ │ ├── sphx_glr_plot_vi_customisation_009.png │ │ ├── sphx_glr_plot_vi_customisation_010.png │ │ ├── sphx_glr_plot_vi_customisation_011.png │ │ ├── sphx_glr_plot_vi_customisation_012.png │ │ ├── sphx_glr_plot_vi_customisation_013.png │ │ ├── sphx_glr_plot_vi_customisation_014.png │ │ ├── sphx_glr_plot_vi_customisation_015.png │ │ ├── sphx_glr_plot_vi_customisation_016.png │ │ ├── sphx_glr_plot_vi_customisation_017.png │ │ ├── sphx_glr_plot_vi_customisation_018.png │ │ ├── sphx_glr_plot_vi_customisation_019.png │ │ ├── sphx_glr_plot_vi_customisation_020.png │ │ ├── sphx_glr_plot_vi_customisation_021.png │ │ ├── sphx_glr_plot_vi_customisation_022.png │ │ ├── sphx_glr_plot_vi_customisation_023.png │ │ ├── sphx_glr_plot_vi_customisation_024.png │ │ ├── sphx_glr_plot_vi_customisation_025.png │ │ ├── sphx_glr_plot_vi_customisation_026.png │ │ ├── sphx_glr_plot_vi_customisation_027.png │ │ ├── sphx_glr_plot_vi_customisation_028.png │ │ ├── sphx_glr_plot_vi_customisation_029.png │ │ ├── sphx_glr_plot_vi_customisation_030.png │ │ ├── sphx_glr_plot_vi_customisation_031.png │ │ ├── sphx_glr_plot_vi_customisation_032.png │ │ └── sphx_glr_plot_vi_customisation_thumb.png │ │ ├── _modules │ │ ├── index.html │ │ └── ramanspy │ │ │ ├── analysis │ │ │ ├── cluster.html │ │ │ ├── decompose.html │ │ │ └── unmix.html │ │ │ ├── core.html │ │ │ ├── datasets.html │ │ │ ├── load.html │ │ │ ├── metrics.html │ │ │ ├── plot │ │ │ └── plot.html │ │ │ ├── preprocessing │ │ │ ├── Pipeline.html │ │ │ ├── Step.html │ │ │ ├── baseline.html │ │ │ ├── denoise.html │ │ │ ├── despike.html │ │ │ ├── misc.html │ │ │ ├── normalise.html │ │ │ └── protocols.html │ │ │ └── synth │ │ │ ├── mix.html │ │ │ └── synth.html │ │ ├── _sources │ │ ├── _autosummary │ │ │ └── ramanspy.preprocessing.denoise.rst.txt │ │ ├── _templates │ │ │ └── autosummary │ │ │ │ └── class.rst.txt │ │ ├── analysis.rst.txt │ │ ├── auto_examples │ │ │ ├── index.rst.txt │ │ │ ├── plot_i_package_overview.rst.txt │ │ │ ├── plot_i_preprocessing_pipelines.rst.txt │ │ │ ├── plot_ii_dl_denoising.rst.txt │ │ │ ├── plot_iii_bacteria_classification.rst.txt │ │ │ └── sg_execution_times.rst.txt │ │ ├── auto_tutorials │ │ │ ├── i-classes │ │ │ │ ├── plot_i_generic_container.rst.txt │ │ │ │ ├── plot_ii_spectrum_container.rst.txt │ │ │ │ ├── plot_iii_image_container.rst.txt │ │ │ │ ├── plot_iv_volume_container.rst.txt │ │ │ │ └── sg_execution_times.rst.txt │ │ │ ├── ii-instrumental │ │ │ │ ├── i_witec.rst.txt │ │ │ │ ├── ii_renishaw.rst.txt │ │ │ │ ├── iii_ocean_insight.rst.txt │ │ │ │ └── iv_other.rst.txt │ │ │ ├── iii-datasets │ │ │ │ ├── ii_rruff.rst.txt │ │ │ │ ├── plot_i_bacteria.rst.txt │ │ │ │ ├── plot_ii_metrics.rst.txt │ │ │ │ └── sg_execution_times.rst.txt │ │ │ ├── index.rst.txt │ │ │ ├── iv-viz │ │ │ │ ├── plot_i_spectra.rst.txt │ │ │ │ ├── plot_ii_mean_spectra.rst.txt │ │ │ │ ├── plot_ii_peaks.rst.txt │ │ │ │ ├── plot_ii_spectra_mean.rst.txt │ │ │ │ ├── plot_iii_image.rst.txt │ │ │ │ ├── plot_iv_volume.rst.txt │ │ │ │ ├── plot_v_peak_dist.rst.txt │ │ │ │ ├── plot_vi_customisation.rst.txt │ │ │ │ └── sg_execution_times.rst.txt │ │ │ ├── v-preprocessing │ │ │ │ ├── plot_i_predefined_methods.rst.txt │ │ │ │ ├── plot_ii_custom_method.rst.txt │ │ │ │ ├── plot_iii_custom_pipeline.rst.txt │ │ │ │ ├── plot_iv_predefined_pipeline.rst.txt │ │ │ │ └── sg_execution_times.rst.txt │ │ │ ├── vi-analysis │ │ │ │ ├── plot_i_decomposition.rst.txt │ │ │ │ ├── plot_ii_kmeans.rst.txt │ │ │ │ ├── plot_iii_unmixing.rst.txt │ │ │ │ ├── plot_iv_integrative_svm.rst.txt │ │ │ │ ├── plot_v_integrative_nn.rst.txt │ │ │ │ └── sg_execution_times.rst.txt │ │ │ └── vii-synth │ │ │ │ ├── plot_i_endmembers.rst.txt │ │ │ │ └── sg_execution_times.rst.txt │ │ ├── data_classes.rst.txt │ │ ├── datasets.rst.txt │ │ ├── denoising │ │ │ ├── ramanspy.preprocessing.denoise.Gaussian.apply.rst.txt │ │ │ ├── ramanspy.preprocessing.denoise.Gaussian.rst.txt │ │ │ ├── ramanspy.preprocessing.denoise.Kernel.apply.rst.txt │ │ │ ├── ramanspy.preprocessing.denoise.Kernel.rst.txt │ │ │ ├── ramanspy.preprocessing.denoise.SavGol.apply.rst.txt │ │ │ ├── ramanspy.preprocessing.denoise.SavGol.rst.txt │ │ │ ├── ramanspy.preprocessing.denoise.Whittaker.apply.rst.txt │ │ │ └── ramanspy.preprocessing.denoise.Whittaker.rst.txt │ │ ├── examples │ │ │ └── README.rst.txt │ │ ├── generated │ │ │ ├── analysis │ │ │ │ ├── cluster │ │ │ │ │ ├── ramanspy.analysis.cluster.KMeans.apply.rst.txt │ │ │ │ │ └── ramanspy.analysis.cluster.KMeans.rst.txt │ │ │ │ ├── decompose │ │ │ │ │ ├── ramanspy.analysis.decompose.ICA.apply.rst.txt │ │ │ │ │ ├── ramanspy.analysis.decompose.ICA.rst.txt │ │ │ │ │ ├── ramanspy.analysis.decompose.NMF.apply.rst.txt │ │ │ │ │ ├── ramanspy.analysis.decompose.NMF.rst.txt │ │ │ │ │ ├── ramanspy.analysis.decompose.PCA.apply.rst.txt │ │ │ │ │ └── ramanspy.analysis.decompose.PCA.rst.txt │ │ │ │ └── unmix │ │ │ │ │ ├── ramanspy.analysis.unmix.FIPPI.apply.rst.txt │ │ │ │ │ ├── ramanspy.analysis.unmix.FIPPI.rst.txt │ │ │ │ │ ├── ramanspy.analysis.unmix.NFINDR.apply.rst.txt │ │ │ │ │ ├── ramanspy.analysis.unmix.NFINDR.rst.txt │ │ │ │ │ ├── ramanspy.analysis.unmix.PPI.apply.rst.txt │ │ │ │ │ ├── ramanspy.analysis.unmix.PPI.rst.txt │ │ │ │ │ ├── ramanspy.analysis.unmix.VCA.apply.rst.txt │ │ │ │ │ └── ramanspy.analysis.unmix.VCA.rst.txt │ │ │ ├── denoising │ │ │ │ ├── ramanspy.preprocessing.denoise.Gaussian.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.Gaussian.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.Kernel.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.Kernel.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.SavGol.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.SavGol.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.Whittaker.apply.rst.txt │ │ │ │ └── ramanspy.preprocessing.denoise.Whittaker.rst.txt │ │ │ └── prepprocessing │ │ │ │ ├── baseline │ │ │ │ ├── ramanspy.preprocessing.baseline.AIRPLS.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.AIRPLS.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.ARPLS.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.ARPLS.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.ASLS.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.ASLS.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.ASPLS.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.ASPLS.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.CornerCutting.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.CornerCutting.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.DRPLS.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.DRPLS.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.FABC.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.FABC.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.Goldindec.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.Goldindec.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.IARPLS.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.IARPLS.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.IASLS.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.IASLS.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.IRSQR.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.IRSQR.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.ModPoly.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.ModPoly.rst.txt │ │ │ │ ├── ramanspy.preprocessing.baseline.Poly.apply.rst.txt │ │ │ │ └── ramanspy.preprocessing.baseline.Poly.rst.txt │ │ │ │ ├── denoising │ │ │ │ ├── ramanspy.preprocessing.denoise.Gaussian.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.Gaussian.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.Kernel.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.Kernel.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.SavGol.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.SavGol.rst.txt │ │ │ │ ├── ramanspy.preprocessing.denoise.Whittaker.apply.rst.txt │ │ │ │ └── ramanspy.preprocessing.denoise.Whittaker.rst.txt │ │ │ │ ├── despiking │ │ │ │ ├── ramanspy.preprocessing.despike.WhitakerHayes.apply.rst.txt │ │ │ │ └── ramanspy.preprocessing.despike.WhitakerHayes.rst.txt │ │ │ │ ├── misc │ │ │ │ ├── ramanspy.preprocessing.misc.BackgroundSubtractor.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.misc.BackgroundSubtractor.rst.txt │ │ │ │ ├── ramanspy.preprocessing.misc.Cropper.apply.rst.txt │ │ │ │ └── ramanspy.preprocessing.misc.Cropper.rst.txt │ │ │ │ ├── norm │ │ │ │ ├── ramanspy.preprocessing.normalise.AUC.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.normalise.AUC.rst.txt │ │ │ │ ├── ramanspy.preprocessing.normalise.MaxIntensity.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.normalise.MaxIntensity.rst.txt │ │ │ │ ├── ramanspy.preprocessing.normalise.MinMax.apply.rst.txt │ │ │ │ ├── ramanspy.preprocessing.normalise.MinMax.rst.txt │ │ │ │ ├── ramanspy.preprocessing.normalise.Vector.apply.rst.txt │ │ │ │ └── ramanspy.preprocessing.normalise.Vector.rst.txt │ │ │ │ └── protocols │ │ │ │ ├── ramanspy.preprocessing.protocols.articular_cartilage.rst.txt │ │ │ │ ├── ramanspy.preprocessing.protocols.bergholt2016.rst.txt │ │ │ │ ├── ramanspy.preprocessing.protocols.default.rst.txt │ │ │ │ ├── ramanspy.preprocessing.protocols.default_fingerprint.rst.txt │ │ │ │ ├── ramanspy.preprocessing.protocols.georgiev2023_P1.rst.txt │ │ │ │ └── ramanspy.preprocessing.protocols.georgiev2023_P3.rst.txt │ │ ├── index.rst.txt │ │ ├── installation.rst.txt │ │ ├── loading.rst.txt │ │ ├── metrics.rst.txt │ │ ├── overview.rst.txt │ │ ├── plot.rst.txt │ │ ├── preprocessing.rst.txt │ │ ├── ramanspy.preprocessing.denoise.Gaussian.apply.rst.txt │ │ ├── ramanspy.preprocessing.denoise.Gaussian.rst.txt │ │ ├── ramanspy.preprocessing.denoise.Kernel.apply.rst.txt │ │ ├── ramanspy.preprocessing.denoise.Kernel.rst.txt │ │ ├── ramanspy.preprocessing.denoise.SavGol.apply.rst.txt │ │ ├── ramanspy.preprocessing.denoise.SavGol.rst.txt │ │ ├── ramanspy.preprocessing.denoise.Whittaker.apply.rst.txt │ │ ├── ramanspy.preprocessing.denoise.Whittaker.rst.txt │ │ ├── ramanspy.preprocessing.denoise.rst.txt │ │ ├── synth.rst.txt │ │ ├── tutorials │ │ │ ├── README.rst.txt │ │ │ ├── i-classes │ │ │ │ └── README.rst.txt │ │ │ ├── ii-instrumental │ │ │ │ └── README.rst.txt │ │ │ ├── iii-datasets │ │ │ │ ├── -README.rst.txt │ │ │ │ └── README.rst.txt │ │ │ ├── iv-viz │ │ │ │ └── README.rst.txt │ │ │ ├── v-preprocessing │ │ │ │ └── README.rst.txt │ │ │ ├── vi-analysis │ │ │ │ └── README.rst.txt │ │ │ └── vii-synth │ │ │ │ └── README.rst.txt │ │ └── viz.rst.txt │ │ ├── _static │ │ ├── _sphinx_javascript_frameworks_compat.js │ │ ├── basic.css │ │ ├── binder_badge_logo.svg │ │ ├── broken_example.png │ │ ├── check-solid.svg │ │ ├── clipboard.min.js │ │ ├── copy-button.svg │ │ ├── copybutton.css │ │ ├── copybutton.js │ │ ├── copybutton_funcs.js │ │ ├── debug.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── jquery-3.6.0.js │ │ ├── jquery.js │ │ ├── jupyterlite_badge_logo.svg │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── no_image.png │ │ ├── plot_directive.css │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── raman_logo_transparent.png │ │ ├── scripts │ │ │ ├── furo-extensions.js │ │ │ ├── furo.js │ │ │ ├── furo.js.LICENSE.txt │ │ │ └── furo.js.map │ │ ├── searchtools.js │ │ ├── sg_gallery-binder.css │ │ ├── sg_gallery-dataframe.css │ │ ├── sg_gallery-rendered-html.css │ │ ├── sg_gallery.css │ │ ├── skeleton.css │ │ ├── sphinx_highlight.js │ │ ├── styles │ │ │ ├── furo-extensions.css │ │ │ ├── furo-extensions.css.map │ │ │ ├── furo.css │ │ │ └── furo.css.map │ │ ├── underscore-1.13.1.js │ │ └── underscore.js │ │ ├── _templates │ │ └── autosummary │ │ │ └── class.html │ │ ├── analysis.html │ │ ├── auto_examples │ │ ├── index.html │ │ ├── plot_i_package_overview.html │ │ ├── plot_i_preprocessing_pipelines.html │ │ ├── plot_ii_dl_denoising.html │ │ ├── plot_iii_bacteria_classification.html │ │ └── sg_execution_times.html │ │ ├── auto_tutorials │ │ ├── i-classes │ │ │ ├── plot_i_generic_container.html │ │ │ ├── plot_ii_spectrum_container.html │ │ │ ├── plot_iii_image_container.html │ │ │ ├── plot_iv_volume_container.html │ │ │ └── sg_execution_times.html │ │ ├── ii-instrumental │ │ │ ├── i_witec.html │ │ │ ├── ii_renishaw.html │ │ │ ├── iii_ocean_insight.html │ │ │ └── iv_other.html │ │ ├── iii-datasets │ │ │ ├── ii_rruff.html │ │ │ ├── plot_i_bacteria.html │ │ │ ├── plot_ii_metrics.html │ │ │ └── sg_execution_times.html │ │ ├── index.html │ │ ├── iv-viz │ │ │ ├── plot_i_spectra.html │ │ │ ├── plot_ii_mean_spectra.html │ │ │ ├── plot_ii_peaks.html │ │ │ ├── plot_ii_spectra_mean.html │ │ │ ├── plot_iii_image.html │ │ │ ├── plot_iv_volume.html │ │ │ ├── plot_v_peak_dist.html │ │ │ ├── plot_vi_customisation.html │ │ │ └── sg_execution_times.html │ │ ├── v-preprocessing │ │ │ ├── plot_i_predefined_methods.html │ │ │ ├── plot_ii_custom_method.html │ │ │ ├── plot_iii_custom_pipeline.html │ │ │ ├── plot_iv_predefined_pipeline.html │ │ │ └── sg_execution_times.html │ │ ├── vi-analysis │ │ │ ├── plot_i_decomposition.html │ │ │ ├── plot_ii_kmeans.html │ │ │ ├── plot_iii_unmixing.html │ │ │ ├── plot_iv_integrative_svm.html │ │ │ ├── plot_v_integrative_nn.html │ │ │ └── sg_execution_times.html │ │ └── vii-synth │ │ │ ├── plot_i_endmembers.html │ │ │ └── sg_execution_times.html │ │ ├── data_classes.html │ │ ├── datasets.html │ │ ├── examples │ │ └── README.html │ │ ├── generated │ │ ├── analysis │ │ │ ├── cluster │ │ │ │ └── ramanspy.analysis.cluster.KMeans.html │ │ │ ├── decompose │ │ │ │ ├── ramanspy.analysis.decompose.ICA.html │ │ │ │ ├── ramanspy.analysis.decompose.NMF.html │ │ │ │ └── ramanspy.analysis.decompose.PCA.html │ │ │ └── unmix │ │ │ │ ├── ramanspy.analysis.unmix.FIPPI.html │ │ │ │ ├── ramanspy.analysis.unmix.NFINDR.html │ │ │ │ ├── ramanspy.analysis.unmix.PPI.html │ │ │ │ └── ramanspy.analysis.unmix.VCA.html │ │ └── prepprocessing │ │ │ ├── baseline │ │ │ ├── ramanspy.preprocessing.baseline.AIRPLS.html │ │ │ ├── ramanspy.preprocessing.baseline.ARPLS.html │ │ │ ├── ramanspy.preprocessing.baseline.ASLS.html │ │ │ ├── ramanspy.preprocessing.baseline.ASPLS.html │ │ │ ├── ramanspy.preprocessing.baseline.CornerCutting.html │ │ │ ├── ramanspy.preprocessing.baseline.DRPLS.html │ │ │ ├── ramanspy.preprocessing.baseline.FABC.html │ │ │ ├── ramanspy.preprocessing.baseline.Goldindec.html │ │ │ ├── ramanspy.preprocessing.baseline.IARPLS.html │ │ │ ├── ramanspy.preprocessing.baseline.IASLS.html │ │ │ ├── ramanspy.preprocessing.baseline.IRSQR.html │ │ │ ├── ramanspy.preprocessing.baseline.ModPoly.html │ │ │ └── ramanspy.preprocessing.baseline.Poly.html │ │ │ ├── denoising │ │ │ ├── ramanspy.preprocessing.denoise.Gaussian.html │ │ │ ├── ramanspy.preprocessing.denoise.Kernel.html │ │ │ ├── ramanspy.preprocessing.denoise.SavGol.html │ │ │ └── ramanspy.preprocessing.denoise.Whittaker.html │ │ │ ├── despiking │ │ │ └── ramanspy.preprocessing.despike.WhitakerHayes.html │ │ │ ├── misc │ │ │ ├── ramanspy.preprocessing.misc.BackgroundSubtractor.html │ │ │ └── ramanspy.preprocessing.misc.Cropper.html │ │ │ ├── norm │ │ │ ├── ramanspy.preprocessing.normalise.AUC.html │ │ │ ├── ramanspy.preprocessing.normalise.MaxIntensity.html │ │ │ ├── ramanspy.preprocessing.normalise.MinMax.html │ │ │ └── ramanspy.preprocessing.normalise.Vector.html │ │ │ └── protocols │ │ │ ├── ramanspy.preprocessing.protocols.bergholt2016.html │ │ │ ├── ramanspy.preprocessing.protocols.georgiev2023_P1.html │ │ │ └── ramanspy.preprocessing.protocols.georgiev2023_P3.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── installation.html │ │ ├── loading.html │ │ ├── metrics.html │ │ ├── objects.inv │ │ ├── overview.html │ │ ├── plot.html │ │ ├── preprocessing.html │ │ ├── search.html │ │ ├── searchindex.js │ │ ├── synth.html │ │ ├── tutorials │ │ ├── README.html │ │ ├── i-classes │ │ │ └── README.html │ │ ├── ii-instrumental │ │ │ └── README.html │ │ ├── iii-datasets │ │ │ ├── -README.html │ │ │ └── README.html │ │ ├── iv-viz │ │ │ └── README.html │ │ ├── v-preprocessing │ │ │ └── README.html │ │ ├── vi-analysis │ │ │ └── README.html │ │ └── vii-synth │ │ │ └── README.html │ │ └── viz.html ├── make.bat └── source │ ├── _templates │ └── autosummary │ │ └── class.rst │ ├── analysis.rst │ ├── auto_examples │ ├── auto_examples_jupyter.zip │ ├── auto_examples_python.zip │ ├── images │ │ ├── sphx_glr_plot_i_package_overview_001.png │ │ ├── sphx_glr_plot_i_package_overview_002.png │ │ ├── sphx_glr_plot_i_package_overview_003.png │ │ ├── sphx_glr_plot_i_package_overview_004.png │ │ ├── sphx_glr_plot_i_package_overview_005.png │ │ ├── sphx_glr_plot_i_package_overview_006.png │ │ ├── sphx_glr_plot_i_package_overview_007.png │ │ ├── sphx_glr_plot_i_package_overview_008.png │ │ ├── sphx_glr_plot_i_package_overview_009.png │ │ ├── sphx_glr_plot_i_package_overview_010.png │ │ ├── sphx_glr_plot_i_package_overview_011.png │ │ ├── sphx_glr_plot_i_package_overview_012.png │ │ ├── sphx_glr_plot_i_package_overview_013.png │ │ ├── sphx_glr_plot_i_package_overview_014.png │ │ ├── sphx_glr_plot_i_package_overview_015.png │ │ ├── sphx_glr_plot_i_package_overview_016.png │ │ ├── sphx_glr_plot_i_package_overview_017.png │ │ ├── sphx_glr_plot_i_package_overview_018.png │ │ ├── sphx_glr_plot_i_package_overview_019.png │ │ ├── sphx_glr_plot_i_package_overview_020.png │ │ ├── sphx_glr_plot_i_package_overview_021.png │ │ ├── sphx_glr_plot_i_package_overview_022.png │ │ ├── sphx_glr_plot_i_package_overview_023.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_001.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_002.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_003.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_004.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_005.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_006.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_007.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_008.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_009.png │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_010.png │ │ ├── sphx_glr_plot_ii_dl_denoising_001.png │ │ ├── sphx_glr_plot_ii_dl_denoising_002.png │ │ ├── sphx_glr_plot_ii_dl_denoising_003.png │ │ ├── sphx_glr_plot_ii_dl_denoising_004.png │ │ ├── sphx_glr_plot_ii_dl_denoising_005.png │ │ ├── sphx_glr_plot_ii_dl_denoising_006.png │ │ ├── sphx_glr_plot_ii_dl_denoising_007.png │ │ ├── sphx_glr_plot_ii_dl_denoising_008.png │ │ ├── sphx_glr_plot_iii_bacteria_classification_001.png │ │ ├── sphx_glr_plot_iii_bacteria_classification_002.png │ │ ├── sphx_glr_plot_iii_bacteria_classification_003.png │ │ ├── sphx_glr_plot_iii_bacteria_classification_004.png │ │ └── thumb │ │ │ ├── sphx_glr_plot_i_package_overview_thumb.png │ │ │ ├── sphx_glr_plot_i_preprocessing_pipelines_thumb.png │ │ │ ├── sphx_glr_plot_ii_dl_denoising_thumb.png │ │ │ └── sphx_glr_plot_iii_bacteria_classification_thumb.png │ ├── index.rst │ ├── plot_i_package_overview.ipynb │ ├── plot_i_package_overview.py │ ├── plot_i_package_overview.py.md5 │ ├── plot_i_package_overview.rst │ ├── plot_i_package_overview_codeobj.pickle │ ├── plot_i_preprocessing_pipelines.ipynb │ ├── plot_i_preprocessing_pipelines.py │ ├── plot_i_preprocessing_pipelines.py.md5 │ ├── plot_i_preprocessing_pipelines.rst │ ├── plot_i_preprocessing_pipelines_codeobj.pickle │ ├── plot_ii_dl_denoising.ipynb │ ├── plot_ii_dl_denoising.py │ ├── plot_ii_dl_denoising.py.md5 │ ├── plot_ii_dl_denoising.rst │ ├── plot_ii_dl_denoising_codeobj.pickle │ ├── plot_iii_bacteria_classification.ipynb │ ├── plot_iii_bacteria_classification.py │ ├── plot_iii_bacteria_classification.py.md5 │ ├── plot_iii_bacteria_classification.rst │ ├── plot_iii_bacteria_classification_codeobj.pickle │ └── sg_execution_times.rst │ ├── auto_tutorials │ ├── auto_tutorials_jupyter.zip │ ├── auto_tutorials_python.zip │ ├── i-classes │ │ ├── images │ │ │ ├── sphx_glr_plot_i_generic_container_001.png │ │ │ ├── sphx_glr_plot_ii_spectrum_container_001.png │ │ │ ├── sphx_glr_plot_iii_image_container_001.png │ │ │ ├── sphx_glr_plot_iii_image_container_002.png │ │ │ ├── sphx_glr_plot_iii_image_container_003.png │ │ │ ├── sphx_glr_plot_iv_volume_container_001.png │ │ │ ├── sphx_glr_plot_iv_volume_container_002.png │ │ │ ├── sphx_glr_plot_iv_volume_container_003.png │ │ │ └── thumb │ │ │ │ ├── sphx_glr_plot_i_generic_container_thumb.png │ │ │ │ ├── sphx_glr_plot_ii_spectrum_container_thumb.png │ │ │ │ ├── sphx_glr_plot_iii_image_container_thumb.png │ │ │ │ └── sphx_glr_plot_iv_volume_container_thumb.png │ │ ├── plot_i_generic_container.ipynb │ │ ├── plot_i_generic_container.py │ │ ├── plot_i_generic_container.py.md5 │ │ ├── plot_i_generic_container.rst │ │ ├── plot_i_generic_container_codeobj.pickle │ │ ├── plot_ii_spectrum_container.ipynb │ │ ├── plot_ii_spectrum_container.py │ │ ├── plot_ii_spectrum_container.py.md5 │ │ ├── plot_ii_spectrum_container.rst │ │ ├── plot_ii_spectrum_container_codeobj.pickle │ │ ├── plot_iii_image_container.ipynb │ │ ├── plot_iii_image_container.py │ │ ├── plot_iii_image_container.py.md5 │ │ ├── plot_iii_image_container.rst │ │ ├── plot_iii_image_container_codeobj.pickle │ │ ├── plot_iv_volume_container.ipynb │ │ ├── plot_iv_volume_container.py │ │ ├── plot_iv_volume_container.py.md5 │ │ ├── plot_iv_volume_container.rst │ │ ├── plot_iv_volume_container_codeobj.pickle │ │ └── sg_execution_times.rst │ ├── ii-instrumental │ │ ├── i_witec.ipynb │ │ ├── i_witec.py │ │ ├── i_witec.rst │ │ ├── i_witec_codeobj.pickle │ │ ├── ii_renishaw.ipynb │ │ ├── ii_renishaw.py │ │ ├── ii_renishaw.rst │ │ ├── ii_renishaw_codeobj.pickle │ │ ├── iii_ocean_insight.ipynb │ │ ├── iii_ocean_insight.py │ │ ├── iii_ocean_insight.rst │ │ ├── iii_ocean_insight_codeobj.pickle │ │ ├── images │ │ │ └── thumb │ │ │ │ ├── sphx_glr_i_witec_thumb.png │ │ │ │ ├── sphx_glr_ii_renishaw_thumb.png │ │ │ │ ├── sphx_glr_iii_ocean_insight_thumb.png │ │ │ │ └── sphx_glr_iv_other_thumb.png │ │ ├── iv_other.ipynb │ │ ├── iv_other.py │ │ ├── iv_other.rst │ │ └── iv_other_codeobj.pickle │ ├── iii-datasets │ │ ├── ii_rruff.ipynb │ │ ├── ii_rruff.py │ │ ├── ii_rruff.rst │ │ ├── ii_rruff_codeobj.pickle │ │ ├── images │ │ │ ├── sphx_glr_plot_i_bacteria_001.png │ │ │ ├── sphx_glr_plot_ii_metrics_001.png │ │ │ └── thumb │ │ │ │ ├── sphx_glr_ii_rruff_thumb.png │ │ │ │ ├── sphx_glr_plot_i_bacteria_thumb.png │ │ │ │ └── sphx_glr_plot_ii_metrics_thumb.png │ │ ├── plot_i_bacteria.ipynb │ │ ├── plot_i_bacteria.py │ │ ├── plot_i_bacteria.py.md5 │ │ ├── plot_i_bacteria.rst │ │ ├── plot_i_bacteria_codeobj.pickle │ │ ├── plot_ii_metrics.ipynb │ │ ├── plot_ii_metrics.py │ │ ├── plot_ii_metrics.py.md5 │ │ ├── plot_ii_metrics.rst │ │ ├── plot_ii_metrics_codeobj.pickle │ │ └── sg_execution_times.rst │ ├── index.rst │ ├── iv-viz │ │ ├── images │ │ │ ├── sphx_glr_plot_i_spectra_001.png │ │ │ ├── sphx_glr_plot_i_spectra_002.png │ │ │ ├── sphx_glr_plot_i_spectra_003.png │ │ │ ├── sphx_glr_plot_i_spectra_004.png │ │ │ ├── sphx_glr_plot_i_spectra_005.png │ │ │ ├── sphx_glr_plot_i_spectra_006.png │ │ │ ├── sphx_glr_plot_i_spectra_007.png │ │ │ ├── sphx_glr_plot_i_spectra_008.png │ │ │ ├── sphx_glr_plot_i_spectra_009.png │ │ │ ├── sphx_glr_plot_i_spectra_010.png │ │ │ ├── sphx_glr_plot_i_spectra_011.png │ │ │ ├── sphx_glr_plot_i_spectra_012.png │ │ │ ├── sphx_glr_plot_i_spectra_013.png │ │ │ ├── sphx_glr_plot_i_spectra_014.png │ │ │ ├── sphx_glr_plot_i_spectra_015.png │ │ │ ├── sphx_glr_plot_ii_peaks_001.png │ │ │ ├── sphx_glr_plot_ii_spectra_mean_001.png │ │ │ ├── sphx_glr_plot_ii_spectra_mean_002.png │ │ │ ├── sphx_glr_plot_ii_spectra_mean_003.png │ │ │ ├── sphx_glr_plot_ii_spectra_mean_004.png │ │ │ ├── sphx_glr_plot_ii_spectra_mean_005.png │ │ │ ├── sphx_glr_plot_ii_spectra_mean_006.png │ │ │ ├── sphx_glr_plot_ii_spectra_mean_007.png │ │ │ ├── sphx_glr_plot_ii_spectra_mean_008.png │ │ │ ├── sphx_glr_plot_ii_spectra_mean_009.png │ │ │ ├── sphx_glr_plot_iii_image_001.png │ │ │ ├── sphx_glr_plot_iii_image_002.png │ │ │ ├── sphx_glr_plot_iii_image_003.png │ │ │ ├── sphx_glr_plot_iii_image_004.png │ │ │ ├── sphx_glr_plot_iii_image_005.png │ │ │ ├── sphx_glr_plot_iii_image_006.png │ │ │ ├── sphx_glr_plot_iv_volume_001.png │ │ │ ├── sphx_glr_plot_iv_volume_002.png │ │ │ ├── sphx_glr_plot_iv_volume_003.png │ │ │ ├── sphx_glr_plot_iv_volume_004.png │ │ │ ├── sphx_glr_plot_v_peak_dist_001.png │ │ │ ├── sphx_glr_plot_v_peak_dist_002.png │ │ │ ├── sphx_glr_plot_v_peak_dist_003.png │ │ │ ├── sphx_glr_plot_v_peak_dist_004.png │ │ │ ├── sphx_glr_plot_v_peak_dist_005.png │ │ │ ├── sphx_glr_plot_vi_customisation_001.png │ │ │ ├── sphx_glr_plot_vi_customisation_002.png │ │ │ ├── sphx_glr_plot_vi_customisation_003.png │ │ │ ├── sphx_glr_plot_vi_customisation_004.png │ │ │ ├── sphx_glr_plot_vi_customisation_005.png │ │ │ ├── sphx_glr_plot_vi_customisation_006.png │ │ │ ├── sphx_glr_plot_vi_customisation_007.png │ │ │ ├── sphx_glr_plot_vi_customisation_008.png │ │ │ ├── sphx_glr_plot_vi_customisation_009.png │ │ │ ├── sphx_glr_plot_vi_customisation_010.png │ │ │ ├── sphx_glr_plot_vi_customisation_011.png │ │ │ ├── sphx_glr_plot_vi_customisation_012.png │ │ │ ├── sphx_glr_plot_vi_customisation_013.png │ │ │ ├── sphx_glr_plot_vi_customisation_014.png │ │ │ ├── sphx_glr_plot_vi_customisation_015.png │ │ │ ├── sphx_glr_plot_vi_customisation_016.png │ │ │ ├── sphx_glr_plot_vi_customisation_017.png │ │ │ ├── sphx_glr_plot_vi_customisation_018.png │ │ │ ├── sphx_glr_plot_vi_customisation_019.png │ │ │ ├── sphx_glr_plot_vi_customisation_020.png │ │ │ ├── sphx_glr_plot_vi_customisation_021.png │ │ │ ├── sphx_glr_plot_vi_customisation_022.png │ │ │ ├── sphx_glr_plot_vi_customisation_023.png │ │ │ ├── sphx_glr_plot_vi_customisation_024.png │ │ │ ├── sphx_glr_plot_vi_customisation_025.png │ │ │ ├── sphx_glr_plot_vi_customisation_026.png │ │ │ ├── sphx_glr_plot_vi_customisation_027.png │ │ │ ├── sphx_glr_plot_vi_customisation_028.png │ │ │ ├── sphx_glr_plot_vi_customisation_029.png │ │ │ ├── sphx_glr_plot_vi_customisation_030.png │ │ │ ├── sphx_glr_plot_vi_customisation_031.png │ │ │ ├── sphx_glr_plot_vi_customisation_032.png │ │ │ └── thumb │ │ │ │ ├── sphx_glr_plot_i_spectra_thumb.png │ │ │ │ ├── sphx_glr_plot_ii_peaks_thumb.png │ │ │ │ ├── sphx_glr_plot_ii_spectra_mean_thumb.png │ │ │ │ ├── sphx_glr_plot_iii_image_thumb.png │ │ │ │ ├── sphx_glr_plot_iv_volume_thumb.png │ │ │ │ ├── sphx_glr_plot_v_peak_dist_thumb.png │ │ │ │ └── sphx_glr_plot_vi_customisation_thumb.png │ │ ├── plot_i_spectra.ipynb │ │ ├── plot_i_spectra.py │ │ ├── plot_i_spectra.py.md5 │ │ ├── plot_i_spectra.rst │ │ ├── plot_i_spectra_codeobj.pickle │ │ ├── plot_ii_peaks.ipynb │ │ ├── plot_ii_peaks.py │ │ ├── plot_ii_peaks.py.md5 │ │ ├── plot_ii_peaks.rst │ │ ├── plot_ii_peaks_codeobj.pickle │ │ ├── plot_ii_spectra_mean.ipynb │ │ ├── plot_ii_spectra_mean.py │ │ ├── plot_ii_spectra_mean.py.md5 │ │ ├── plot_ii_spectra_mean.rst │ │ ├── plot_ii_spectra_mean_codeobj.pickle │ │ ├── plot_iii_image.ipynb │ │ ├── plot_iii_image.py │ │ ├── plot_iii_image.py.md5 │ │ ├── plot_iii_image.rst │ │ ├── plot_iii_image_codeobj.pickle │ │ ├── plot_iv_volume.ipynb │ │ ├── plot_iv_volume.py │ │ ├── plot_iv_volume.py.md5 │ │ ├── plot_iv_volume.rst │ │ ├── plot_iv_volume_codeobj.pickle │ │ ├── plot_v_peak_dist.ipynb │ │ ├── plot_v_peak_dist.py │ │ ├── plot_v_peak_dist.py.md5 │ │ ├── plot_v_peak_dist.rst │ │ ├── plot_v_peak_dist_codeobj.pickle │ │ ├── plot_vi_customisation.ipynb │ │ ├── plot_vi_customisation.py │ │ ├── plot_vi_customisation.py.md5 │ │ ├── plot_vi_customisation.rst │ │ ├── plot_vi_customisation_codeobj.pickle │ │ └── sg_execution_times.rst │ ├── v-preprocessing │ │ ├── images │ │ │ ├── sphx_glr_plot_i_predefined_methods_001.png │ │ │ ├── sphx_glr_plot_i_predefined_methods_002.png │ │ │ ├── sphx_glr_plot_i_predefined_methods_003.png │ │ │ ├── sphx_glr_plot_i_predefined_methods_004.png │ │ │ ├── sphx_glr_plot_i_predefined_methods_005.png │ │ │ ├── sphx_glr_plot_i_predefined_methods_006.png │ │ │ ├── sphx_glr_plot_ii_custom_method_001.png │ │ │ ├── sphx_glr_plot_ii_custom_method_002.png │ │ │ ├── sphx_glr_plot_ii_custom_method_003.png │ │ │ ├── sphx_glr_plot_iii_custom_pipeline_001.png │ │ │ ├── sphx_glr_plot_iii_custom_pipeline_002.png │ │ │ ├── sphx_glr_plot_iii_custom_pipeline_003.png │ │ │ ├── sphx_glr_plot_iii_custom_pipeline_004.png │ │ │ ├── sphx_glr_plot_iii_custom_pipeline_005.png │ │ │ ├── sphx_glr_plot_iii_custom_pipeline_006.png │ │ │ ├── sphx_glr_plot_iv_predefined_pipeline_001.png │ │ │ ├── sphx_glr_plot_iv_predefined_pipeline_002.png │ │ │ └── thumb │ │ │ │ ├── sphx_glr_plot_i_predefined_methods_thumb.png │ │ │ │ ├── sphx_glr_plot_ii_custom_method_thumb.png │ │ │ │ ├── sphx_glr_plot_iii_custom_pipeline_thumb.png │ │ │ │ └── sphx_glr_plot_iv_predefined_pipeline_thumb.png │ │ ├── plot_i_predefined_methods.ipynb │ │ ├── plot_i_predefined_methods.py │ │ ├── plot_i_predefined_methods.py.md5 │ │ ├── plot_i_predefined_methods.rst │ │ ├── plot_i_predefined_methods_codeobj.pickle │ │ ├── plot_ii_custom_method.ipynb │ │ ├── plot_ii_custom_method.py │ │ ├── plot_ii_custom_method.py.md5 │ │ ├── plot_ii_custom_method.rst │ │ ├── plot_ii_custom_method_codeobj.pickle │ │ ├── plot_iii_custom_pipeline.ipynb │ │ ├── plot_iii_custom_pipeline.py │ │ ├── plot_iii_custom_pipeline.py.md5 │ │ ├── plot_iii_custom_pipeline.rst │ │ ├── plot_iii_custom_pipeline_codeobj.pickle │ │ ├── plot_iv_predefined_pipeline.ipynb │ │ ├── plot_iv_predefined_pipeline.py │ │ ├── plot_iv_predefined_pipeline.py.md5 │ │ ├── plot_iv_predefined_pipeline.rst │ │ ├── plot_iv_predefined_pipeline_codeobj.pickle │ │ └── sg_execution_times.rst │ ├── vi-analysis │ │ ├── images │ │ │ ├── sphx_glr_plot_i_decomposition_001.png │ │ │ ├── sphx_glr_plot_i_decomposition_002.png │ │ │ ├── sphx_glr_plot_i_decomposition_003.png │ │ │ ├── sphx_glr_plot_i_decomposition_004.png │ │ │ ├── sphx_glr_plot_i_decomposition_005.png │ │ │ ├── sphx_glr_plot_i_decomposition_006.png │ │ │ ├── sphx_glr_plot_i_decomposition_007.png │ │ │ ├── sphx_glr_plot_i_decomposition_008.png │ │ │ ├── sphx_glr_plot_i_decomposition_009.png │ │ │ ├── sphx_glr_plot_ii_kmeans_001.png │ │ │ ├── sphx_glr_plot_ii_kmeans_002.png │ │ │ ├── sphx_glr_plot_ii_kmeans_003.png │ │ │ ├── sphx_glr_plot_ii_kmeans_004.png │ │ │ ├── sphx_glr_plot_ii_kmeans_005.png │ │ │ ├── sphx_glr_plot_ii_kmeans_006.png │ │ │ ├── sphx_glr_plot_iii_unmixing_001.png │ │ │ ├── sphx_glr_plot_iii_unmixing_002.png │ │ │ ├── sphx_glr_plot_iii_unmixing_003.png │ │ │ ├── sphx_glr_plot_iii_unmixing_004.png │ │ │ ├── sphx_glr_plot_iii_unmixing_005.png │ │ │ ├── sphx_glr_plot_iii_unmixing_006.png │ │ │ ├── sphx_glr_plot_iii_unmixing_007.png │ │ │ ├── sphx_glr_plot_iii_unmixing_008.png │ │ │ ├── sphx_glr_plot_iii_unmixing_009.png │ │ │ ├── sphx_glr_plot_iv_integrative_svm_001.png │ │ │ ├── sphx_glr_plot_v_integrative_nn_001.png │ │ │ ├── sphx_glr_plot_v_integrative_nn_002.png │ │ │ ├── sphx_glr_plot_v_integrative_nn_003.png │ │ │ └── thumb │ │ │ │ ├── sphx_glr_plot_i_decomposition_thumb.png │ │ │ │ ├── sphx_glr_plot_ii_kmeans_thumb.png │ │ │ │ ├── sphx_glr_plot_iii_unmixing_thumb.png │ │ │ │ ├── sphx_glr_plot_iv_integrative_svm_thumb.png │ │ │ │ └── sphx_glr_plot_v_integrative_nn_thumb.png │ │ ├── plot_i_decomposition.ipynb │ │ ├── plot_i_decomposition.py │ │ ├── plot_i_decomposition.py.md5 │ │ ├── plot_i_decomposition.rst │ │ ├── plot_i_decomposition_codeobj.pickle │ │ ├── plot_ii_kmeans.ipynb │ │ ├── plot_ii_kmeans.py │ │ ├── plot_ii_kmeans.py.md5 │ │ ├── plot_ii_kmeans.rst │ │ ├── plot_ii_kmeans_codeobj.pickle │ │ ├── plot_iii_unmixing.ipynb │ │ ├── plot_iii_unmixing.py │ │ ├── plot_iii_unmixing.py.md5 │ │ ├── plot_iii_unmixing.rst │ │ ├── plot_iii_unmixing_codeobj.pickle │ │ ├── plot_iv_integrative_svm.ipynb │ │ ├── plot_iv_integrative_svm.py │ │ ├── plot_iv_integrative_svm.py.md5 │ │ ├── plot_iv_integrative_svm.rst │ │ ├── plot_iv_integrative_svm_codeobj.pickle │ │ ├── plot_v_integrative_nn.ipynb │ │ ├── plot_v_integrative_nn.py │ │ ├── plot_v_integrative_nn.py.md5 │ │ ├── plot_v_integrative_nn.rst │ │ ├── plot_v_integrative_nn_codeobj.pickle │ │ └── sg_execution_times.rst │ └── vii-synth │ │ ├── images │ │ ├── sphx_glr_plot_i_endmembers_001.png │ │ └── thumb │ │ │ └── sphx_glr_plot_i_endmembers_thumb.png │ │ ├── plot_i_endmembers.ipynb │ │ ├── plot_i_endmembers.py │ │ ├── plot_i_endmembers.py.md5 │ │ ├── plot_i_endmembers.rst │ │ ├── plot_i_endmembers_codeobj.pickle │ │ └── sg_execution_times.rst │ ├── conf.py │ ├── data_classes.rst │ ├── datasets.rst │ ├── examples │ ├── 3D THP1 map 001 L5 (B+R) (Sub BG).mat │ ├── README.rst │ ├── ResUNet.pt │ ├── plot_i_package_overview.py │ ├── plot_i_preprocessing_pipelines.py │ ├── plot_ii_dl_denoising.py │ └── plot_iii_bacteria_classification.py │ ├── generated │ ├── analysis │ │ ├── cluster │ │ │ └── ramanspy.analysis.cluster.KMeans.rst │ │ ├── decompose │ │ │ ├── ramanspy.analysis.decompose.ICA.rst │ │ │ ├── ramanspy.analysis.decompose.NMF.rst │ │ │ └── ramanspy.analysis.decompose.PCA.rst │ │ └── unmix │ │ │ ├── ramanspy.analysis.unmix.FIPPI.rst │ │ │ ├── ramanspy.analysis.unmix.NFINDR.rst │ │ │ ├── ramanspy.analysis.unmix.PPI.rst │ │ │ └── ramanspy.analysis.unmix.VCA.rst │ └── prepprocessing │ │ ├── baseline │ │ ├── ramanspy.preprocessing.baseline.AIRPLS.rst │ │ ├── ramanspy.preprocessing.baseline.ARPLS.rst │ │ ├── ramanspy.preprocessing.baseline.ASLS.rst │ │ ├── ramanspy.preprocessing.baseline.ASPLS.rst │ │ ├── ramanspy.preprocessing.baseline.CornerCutting.rst │ │ ├── ramanspy.preprocessing.baseline.DRPLS.rst │ │ ├── ramanspy.preprocessing.baseline.FABC.rst │ │ ├── ramanspy.preprocessing.baseline.Goldindec.rst │ │ ├── ramanspy.preprocessing.baseline.IARPLS.rst │ │ ├── ramanspy.preprocessing.baseline.IASLS.rst │ │ ├── ramanspy.preprocessing.baseline.IRSQR.rst │ │ ├── ramanspy.preprocessing.baseline.ModPoly.rst │ │ └── ramanspy.preprocessing.baseline.Poly.rst │ │ ├── denoising │ │ ├── ramanspy.preprocessing.denoise.Gaussian.rst │ │ ├── ramanspy.preprocessing.denoise.Kernel.rst │ │ ├── ramanspy.preprocessing.denoise.SavGol.rst │ │ └── ramanspy.preprocessing.denoise.Whittaker.rst │ │ ├── despiking │ │ └── ramanspy.preprocessing.despike.WhitakerHayes.rst │ │ ├── misc │ │ ├── ramanspy.preprocessing.misc.BackgroundSubtractor.rst │ │ └── ramanspy.preprocessing.misc.Cropper.rst │ │ ├── norm │ │ ├── ramanspy.preprocessing.normalise.AUC.rst │ │ ├── ramanspy.preprocessing.normalise.MaxIntensity.rst │ │ ├── ramanspy.preprocessing.normalise.MinMax.rst │ │ └── ramanspy.preprocessing.normalise.Vector.rst │ │ └── protocols │ │ ├── ramanspy.preprocessing.protocols.bergholt2016.rst │ │ ├── ramanspy.preprocessing.protocols.georgiev2023_P1.rst │ │ └── ramanspy.preprocessing.protocols.georgiev2023_P3.rst │ ├── images │ ├── raman_logo_transparent.png │ └── ramanspy_graphical_abstract.png │ ├── index.rst │ ├── installation.rst │ ├── loading.rst │ ├── metrics.rst │ ├── overview.rst │ ├── plot.rst │ ├── preprocessing.rst │ ├── synth.rst │ └── tutorials │ ├── README.rst │ ├── i-classes │ ├── README.rst │ ├── my_raman_image │ ├── plot_i_generic_container.py │ ├── plot_ii_spectrum_container.py │ ├── plot_iii_image_container.py │ └── plot_iv_volume_container.py │ ├── ii-instrumental │ ├── README.rst │ ├── i_witec.py │ ├── ii_renishaw.py │ ├── iii_ocean_insight.py │ └── iv_other.py │ ├── iii-datasets │ ├── README.rst │ ├── ii_rruff.py │ ├── plot_i_bacteria.py │ └── plot_ii_metrics.py │ ├── iv-viz │ ├── README.rst │ ├── cell_image.png │ ├── plot_i_spectra.py │ ├── plot_ii_peaks.py │ ├── plot_ii_spectra_mean.py │ ├── plot_iii_image.py │ ├── plot_iv_volume.py │ ├── plot_v_peak_dist.py │ ├── plot_vi_customisation.py │ └── v.png │ ├── v-preprocessing │ ├── README.rst │ ├── plot_i_predefined_methods.py │ ├── plot_ii_custom_method.py │ ├── plot_iii_custom_pipeline.py │ └── plot_iv_predefined_pipeline.py │ ├── vi-analysis │ ├── README.rst │ ├── plot_i_decomposition.py │ ├── plot_ii_kmeans.py │ ├── plot_iii_unmixing.py │ ├── plot_iv_integrative_svm.py │ └── plot_v_integrative_nn.py │ └── vii-synth │ ├── README.rst │ └── 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