spacr 0.0.36__py3-none-any.whl → 0.0.62__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (33) hide show
  1. spacr/__init__.py +11 -4
  2. spacr/__main__.py +0 -2
  3. spacr/alpha.py +514 -2
  4. spacr/annotate_app.py +112 -116
  5. spacr/core.py +864 -728
  6. spacr/deep_spacr.py +696 -0
  7. spacr/foldseek.py +2 -16
  8. spacr/graph_learning.py +297 -253
  9. spacr/gui.py +9 -8
  10. spacr/gui_2.py +90 -0
  11. spacr/gui_classify_app.py +3 -4
  12. spacr/gui_mask_app.py +9 -9
  13. spacr/gui_measure_app.py +3 -5
  14. spacr/gui_utils.py +132 -33
  15. spacr/io.py +308 -464
  16. spacr/mask_app.py +109 -5
  17. spacr/measure.py +15 -1
  18. spacr/models/cp/toxo_pv_lumen.CP_model +0 -0
  19. spacr/old_code.py +69 -1
  20. spacr/plot.py +23 -6
  21. spacr/sequencing.py +1130 -0
  22. spacr/sim.py +0 -42
  23. spacr/timelapse.py +0 -1
  24. spacr/train.py +172 -13
  25. spacr/umap.py +0 -689
  26. spacr/utils.py +1322 -75
  27. {spacr-0.0.36.dist-info → spacr-0.0.62.dist-info}/METADATA +14 -29
  28. spacr-0.0.62.dist-info/RECORD +39 -0
  29. {spacr-0.0.36.dist-info → spacr-0.0.62.dist-info}/entry_points.txt +1 -0
  30. spacr-0.0.36.dist-info/RECORD +0 -35
  31. {spacr-0.0.36.dist-info → spacr-0.0.62.dist-info}/LICENSE +0 -0
  32. {spacr-0.0.36.dist-info → spacr-0.0.62.dist-info}/WHEEL +0 -0
  33. {spacr-0.0.36.dist-info → spacr-0.0.62.dist-info}/top_level.txt +0 -0
{spacr-0.0.36.dist-info → spacr-0.0.62.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: spacr
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- Version: 0.0.36
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+ Version: 0.0.62
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  Summary: Spatial phenotype analysis of crisp screens (SpaCr)
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  Home-page: https://github.com/EinarOlafsson/spacr
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  Author: Einar Birnir Olafsson
@@ -9,10 +9,11 @@ Classifier: Programming Language :: Python :: 3
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  Classifier: License :: OSI Approved :: MIT License
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  Classifier: Operating System :: OS Independent
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  License-File: LICENSE
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+ Requires-Dist: dgl
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  Requires-Dist: torch >=2.2.1
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  Requires-Dist: torchvision >=0.17.1
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  Requires-Dist: torch-geometric >=2.5.1
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- Requires-Dist: numpy >=1.26.4
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+ Requires-Dist: numpy <2.0,>=1.26.4
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  Requires-Dist: pandas >=2.2.1
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  Requires-Dist: statsmodels >=0.14.1
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  Requires-Dist: scikit-image >=0.22.0
@@ -30,10 +31,13 @@ Requires-Dist: trackpy >=0.6.2
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  Requires-Dist: cellpose >=3.0.6
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  Requires-Dist: IPython >=8.18.1
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  Requires-Dist: opencv-python-headless >=4.9.0.80
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- Requires-Dist: umap >=0.1.1
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+ Requires-Dist: umap-learn >=0.5.6
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  Requires-Dist: ttkthemes >=3.2.2
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  Requires-Dist: xgboost >=2.0.3
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  Requires-Dist: PyWavelets >=1.6.0
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+ Requires-Dist: torchcam >=0.4.0
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+ Requires-Dist: ttf-opensans >=2020.10.30
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+ Requires-Dist: customtkinter >=5.2.2
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  Requires-Dist: lxml >=5.1.0
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  Provides-Extra: dev
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  Requires-Dist: pytest >=3.9 ; extra == 'dev'
@@ -65,9 +69,9 @@ Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organizat
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  ## Features
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- - **Generate Masks:** Generate cellpose masks for cells, nuclei and pathogen images.
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+ - **Generate Masks:** Generate cellpose masks of cell, nuclei and pathogen objects.
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- - **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity quantiles, shannon-entropy, pearsons and manders correlation, homogenicity and radial distribution. Measurements are saved to a sql database in object level tables.
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+ - **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogenicity and radial distribution. Measurements are saved to a sql database in object level tables.
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  - **Crop Images:** Objects (e.g. cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in an sql database that can be annotated and used to train CNNs/Transformer models for classefication tasks.
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@@ -81,11 +85,13 @@ Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organizat
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  - **Simulations:** Simulate spatial phenotype screens.
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+ - **Sequencing:** Map FASTQ reads to barecode and gRNA barecode metadata.
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+
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  - **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
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  ## Installation
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- spacr requires Tkinter for its graphical user interface features.
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+ Requires Tkinter for graphical user interface features.
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  ### Ubuntu
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@@ -105,29 +111,8 @@ install spacr with pip
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  pip install spacr
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  ```
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- To run spacr GUIs after installing spacr:
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+ Run spacr GUI:
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- To generate masks:
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- ```
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- gui_mask
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- ```
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- To generate measurements and cropped images:
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- ```
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- gui_measure
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- ```
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- To curate masks for finetuning cellpose models:
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- ```
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- gui_make_masks
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- ```
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- To annotate paths to images in sql database created in gui_measure:
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- ```
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- gui_annotate
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- ```
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- Train torch CNNs/Transformers to classify single object images.
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- ```
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- gui_classify
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- ```
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- Simulate spatial phenotype screens.
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  ```
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- gui_sim
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+ gui
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  ```
spacr-0.0.62.dist-info/RECORD ADDED
@@ -0,0 +1,39 @@
1
+ spacr/__init__.py,sha256=64QJU2_IUd_40TTKQ2j239rF3PJP_gyciL_rolQOxuU,1144
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+ spacr/__main__.py,sha256=L3Dnk-YG3lULeaMxD1mS-_t89g4qWrJ7bnpBvNiQhUE,283
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+ spacr/alpha.py,sha256=Y95sLEfpK2OSYKRn3M8eUOU33JJeXfV8zhrC4KnwSTY,35244
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+ spacr/annotate_app.py,sha256=_KlDYbnaKr_VvghMWSr6gWbP_lByPghGLiCfEIJ48so,19500
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+ spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
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+ spacr/cli.py,sha256=507jfOOEV8BoL4eeUcblvH-iiDHdBrEVJLu1ghAAPSc,1800
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+ spacr/core.py,sha256=EIhsuSyJQPxq1UfH3VNh3ubt403W1Ahvnz44pX35BCc,166307
8
+ spacr/deep_spacr.py,sha256=ljIakns6q74an5QwDU7j0xoj6jRCAz-ejY0QHj9X0d8,33193
9
+ spacr/foldseek.py,sha256=w7M7qRYvP5syJlPErQkHzPLOkiyLN77E0XyL3NiFZwI,33540
10
+ spacr/get_alfafold_structures.py,sha256=n0g8gne-oyAV3Uo6qxZoJq5X1cUUyD8u0pOC_W2PX40,3541
11
+ spacr/graph_learning.py,sha256=M7KW1J72LA4hLfVNVBOqxf_4z9tXi-UyoZfhaLJXqSE,11986
12
+ spacr/graph_learning_lap.py,sha256=MyNRLb63gsjBlui-ByZ0anHugYulL6M-OsGm8rnGBmE,3385
13
+ spacr/gui.py,sha256=zu-i8ezLJ03jNRACK7CRgNhkM8g8-pJFwZ-OSDFzsPg,6498
14
+ spacr/gui_2.py,sha256=FPlmvGm1VIood_YBnG44IafgjjaVfagybTnjVEOs5Ig,3299
15
+ spacr/gui_classify_app.py,sha256=LY33wott1mR7AFYwBI9ZQZYY16lBB-wuaY4pL_poaQ0,7884
16
+ spacr/gui_mask_app.py,sha256=WKkAH0jv-SnfaZdJ8MkC7mkUIVSSrNE8lUfH3QBvUak,9747
17
+ spacr/gui_measure_app.py,sha256=5vjjds5NFaOcE8XeuWDug9k-NI4jbTrwp54sJ7DNaNI,9625
18
+ spacr/gui_sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ spacr/gui_utils.py,sha256=JRWwmGEEVSPgs0UtZRukdNwIUJepbP675_Fvs5qocPk,49718
20
+ spacr/io.py,sha256=8jpnsUOZMxfhGamduiq4BXgUtfh80kF4R_S-8N3EIrw,109305
21
+ spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
22
+ spacr/mask_app.py,sha256=jlKmj_evveIkkyH3PYEcAshcLXN0DOPWB1oc4hAwq9E,44201
23
+ spacr/measure.py,sha256=KOBmrVE9nrKwIoXG16wV1sy5nSj9EOa_FhK7i431V-A,55325
24
+ spacr/old_code.py,sha256=jw67DAGoLBd7mWofVzRJSEmCI1Qrff26zIo65SEkV00,13817
25
+ spacr/plot.py,sha256=9tQEDDIHzex-T90VaS_PfcHwbWfYEYfMeKkgEdlK6ko,62045
26
+ spacr/sequencing.py,sha256=OiRK6gpEkuEhKoUJcU-BXWDmz4RkDxKeJCE_C6w1zJc,50503
27
+ spacr/sim.py,sha256=fpkOs-VBU40xBFuSoO97aTewQWPSYolg5C_PkjeQm_Y,71344
28
+ spacr/timelapse.py,sha256=5TNmkzR_urMxy0eVB4quGdjNj2QduyiwrLL2I-udlAg,39614
29
+ spacr/train.py,sha256=rpOJBu3ho0Oec37I1mO4_3eQ480y_4bgFiKCOgiyN8s,31741
30
+ spacr/umap.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
31
+ spacr/utils.py,sha256=zX6zhS7UmCOA2JzBw4uDb-p0SPq5igaeYjzJ56d7hG8,171627
32
+ spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
33
+ spacr/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
34
+ spacr-0.0.62.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
35
+ spacr-0.0.62.dist-info/METADATA,sha256=gDnAj_Lo8ZAUejMSrwX5JWvvkJKzIdbIxenK36dqXms,4767
36
+ spacr-0.0.62.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
37
+ spacr-0.0.62.dist-info/entry_points.txt,sha256=xncHsqD9MI5wj0_p4mgZlrB8dHm_g_qF0Ggo1c78LqY,315
38
+ spacr-0.0.62.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
39
+ spacr-0.0.62.dist-info/RECORD,,
{spacr-0.0.36.dist-info → spacr-0.0.62.dist-info}/entry_points.txt RENAMED
@@ -2,6 +2,7 @@
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  annotate = spacr.annotate_app:gui_annotation
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  classify = spacr.gui_classify_app:gui_classify
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  gui = spacr.gui:gui_app
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+ gui2 = spacr.gui_2:gui_app
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  make_masks = spacr.mask_app:gui_make_masks
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  mask = spacr.gui_mask_app:gui_mask
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  measure = spacr.gui_measure_app:gui_measure
spacr-0.0.36.dist-info/RECORD DELETED
@@ -1,35 +0,0 @@
1
- spacr/__init__.py,sha256=mDi-Qu5r1vZnqIbUBV1JAoSq-mxmMEOmni1JSG2e4Wo,879
2
- spacr/__main__.py,sha256=_qRkhbFrH_cXr7AZs6KHL8Hh4VApqNdpNCtiKn2ePTo,285
3
- spacr/alpha.py,sha256=1LUtTaeVHqcTMxoCMA7mlsNYyaR0KEaXglwXsUQLwKo,13776
4
- spacr/annotate_app.py,sha256=oP3aHbtWyvlg7Hnee5GIHzqeM8Jwf5Y9N2n6bO7ZtfY,20032
5
- spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
6
- spacr/cli.py,sha256=507jfOOEV8BoL4eeUcblvH-iiDHdBrEVJLu1ghAAPSc,1800
7
- spacr/core.py,sha256=_R8gXNnjf680yrnbCi2piWQUz7PDbqWYn7SL5MACLfo,156457
8
- spacr/foldseek.py,sha256=cWtLzvFF2O_mq5I71UMiuU9DTvDCp7wl6aaWAZRrBZc,33970
9
- spacr/get_alfafold_structures.py,sha256=n0g8gne-oyAV3Uo6qxZoJq5X1cUUyD8u0pOC_W2PX40,3541
10
- spacr/graph_learning.py,sha256=sD4eOC7Q16rr7WO20mCi_E16_LqioGUUgPamAHIIeNI,12568
11
- spacr/graph_learning_lap.py,sha256=MyNRLb63gsjBlui-ByZ0anHugYulL6M-OsGm8rnGBmE,3385
12
- spacr/gui.py,sha256=2d2JHYVWhEFUkB3u_2OarCV_V07eLtJKUMKVKuJ7nAo,6430
13
- spacr/gui_classify_app.py,sha256=fWJOQO0NjhymdRxccQYlMVbDKBKEPHbAbU9NEdp0peI,7921
14
- spacr/gui_mask_app.py,sha256=FXSMasIFBUZWXpVXELR21UevK8g65xqLxio9B2xEyYM,9754
15
- spacr/gui_measure_app.py,sha256=tkshD4KOydHTWeViwkjQILowJUVs4PNhBZzy76jxssI,9680
16
- spacr/gui_sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
17
- spacr/gui_utils.py,sha256=f1kyecWyHygw9Eb67PbZ-wWXtn2b85E0LcOLl2Fi3g8,40717
18
- spacr/io.py,sha256=sqWiLtUFiholVSAfMbeK8ssuAl9BiRzgfv9ixMsWDRE,108691
19
- spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
20
- spacr/mask_app.py,sha256=dAMYQLn8jVbtsuoJ98p_Oih_XSMZpdOVPlefgjdVAZM,39378
21
- spacr/measure.py,sha256=bS79LNOfb7j7_qf_lS9NVdO2vcgFsHC8DvPsSgMnvTA,54690
22
- spacr/old_code.py,sha256=ujL-shd353C_Ac74MtzUTEHdpqsDguNwe_5FziUGA-M,11227
23
- spacr/plot.py,sha256=VtDKTJ_zo8CAVC3ILuIN_wUP6197vq089wNZuom7T8g,61655
24
- spacr/sim.py,sha256=2NR5hm--HVcYQnj1SCHoUCVbh_b2XUjjjfoAUIXFwnQ,72997
25
- spacr/timelapse.py,sha256=plPjR8nZ7_Q50VAvMvHK2TUE4F-vh7R23JnI6tSW02g,39661
26
- spacr/train.py,sha256=lp66dWYkiMMlgdYlMjAsJnkIZFWLizKB-xwyVnKgFBs,25904
27
- spacr/umap.py,sha256=4QSrQ16Og-Ijq-SwguMQT2f20UWz1LE5HQeSLmzSl8c,29370
28
- spacr/utils.py,sha256=D3WRf_0w0T6dZHh3BfwScGBQjorljgWW6CQUdM0ToN8,120918
29
- spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
30
- spacr-0.0.36.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
31
- spacr-0.0.36.dist-info/METADATA,sha256=NzLoqcIVHlvAZyDGvBM7lXQXeDGsop8N15bKVFTi3RI,4973
32
- spacr-0.0.36.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
33
- spacr-0.0.36.dist-info/entry_points.txt,sha256=_khj_UcegrI5N29QcgxECsxVsfpVQzG3U5OUoKdtTcw,288
34
- spacr-0.0.36.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
35
- spacr-0.0.36.dist-info/RECORD,,
{spacr-0.0.36.dist-info → spacr-0.0.62.dist-info}/WHEEL RENAMED
File without changes