spacr 0.2.3__tar.gz → 0.2.5__tar.gz

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 (125) hide show
  1. {spacr-0.2.3/spacr.egg-info → spacr-0.2.5}/PKG-INFO +5 -1
  2. {spacr-0.2.3 → spacr-0.2.5}/setup.py +6 -2
  3. {spacr-0.2.3 → spacr-0.2.5}/spacr/app_annotate.py +3 -4
  4. {spacr-0.2.3 → spacr-0.2.5}/spacr/core.py +100 -282
  5. {spacr-0.2.3 → spacr-0.2.5}/spacr/gui.py +20 -38
  6. spacr-0.2.5/spacr/gui_core.py +696 -0
  7. {spacr-0.2.3 → spacr-0.2.5}/spacr/gui_elements.py +395 -60
  8. spacr-0.2.5/spacr/gui_utils.py +640 -0
  9. {spacr-0.2.3 → spacr-0.2.5}/spacr/io.py +130 -50
  10. {spacr-0.2.3 → spacr-0.2.5}/spacr/measure.py +199 -154
  11. {spacr-0.2.3 → spacr-0.2.5}/spacr/plot.py +108 -42
  12. spacr-0.2.5/spacr/resources/font/open_sans/OFL.txt +93 -0
  13. spacr-0.2.5/spacr/resources/font/open_sans/OpenSans-Italic-VariableFont_wdth,wght.ttf +0 -0
  14. spacr-0.2.5/spacr/resources/font/open_sans/OpenSans-VariableFont_wdth,wght.ttf +0 -0
  15. spacr-0.2.5/spacr/resources/font/open_sans/README.txt +100 -0
  16. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-Bold.ttf +0 -0
  17. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-BoldItalic.ttf +0 -0
  18. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-ExtraBold.ttf +0 -0
  19. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-ExtraBoldItalic.ttf +0 -0
  20. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-Italic.ttf +0 -0
  21. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-Light.ttf +0 -0
  22. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-LightItalic.ttf +0 -0
  23. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-Medium.ttf +0 -0
  24. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-MediumItalic.ttf +0 -0
  25. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-Regular.ttf +0 -0
  26. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-SemiBold.ttf +0 -0
  27. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-SemiBoldItalic.ttf +0 -0
  28. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-Bold.ttf +0 -0
  29. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-BoldItalic.ttf +0 -0
  30. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-ExtraBold.ttf +0 -0
  31. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-ExtraBoldItalic.ttf +0 -0
  32. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-Italic.ttf +0 -0
  33. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-Light.ttf +0 -0
  34. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-LightItalic.ttf +0 -0
  35. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-Medium.ttf +0 -0
  36. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-MediumItalic.ttf +0 -0
  37. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-Regular.ttf +0 -0
  38. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-SemiBold.ttf +0 -0
  39. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-SemiBoldItalic.ttf +0 -0
  40. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Bold.ttf +0 -0
  41. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-BoldItalic.ttf +0 -0
  42. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-ExtraBold.ttf +0 -0
  43. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-ExtraBoldItalic.ttf +0 -0
  44. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Italic.ttf +0 -0
  45. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Light.ttf +0 -0
  46. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-LightItalic.ttf +0 -0
  47. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Medium.ttf +0 -0
  48. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-MediumItalic.ttf +0 -0
  49. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Regular.ttf +0 -0
  50. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-SemiBold.ttf +0 -0
  51. spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-SemiBoldItalic.ttf +0 -0
  52. spacr-0.2.5/spacr/resources/icons/logo.pdf +2786 -6
  53. spacr-0.2.5/spacr/resources/icons/logo_spacr.png +0 -0
  54. {spacr-0.2.3 → spacr-0.2.5}/spacr/settings.py +12 -87
  55. {spacr-0.2.3 → spacr-0.2.5}/spacr/utils.py +45 -10
  56. {spacr-0.2.3 → spacr-0.2.5/spacr.egg-info}/PKG-INFO +5 -1
  57. spacr-0.2.5/spacr.egg-info/SOURCES.txt +120 -0
  58. {spacr-0.2.3 → spacr-0.2.5}/spacr.egg-info/requires.txt +4 -0
  59. spacr-0.2.3/spacr/gui_core.py +0 -789
  60. spacr-0.2.3/spacr/gui_utils.py +0 -320
  61. spacr-0.2.3/spacr.egg-info/SOURCES.txt +0 -78
  62. {spacr-0.2.3 → spacr-0.2.5}/LICENSE +0 -0
  63. {spacr-0.2.3 → spacr-0.2.5}/MANIFEST.in +0 -0
  64. {spacr-0.2.3 → spacr-0.2.5}/README.rst +0 -0
  65. {spacr-0.2.3 → spacr-0.2.5}/setup.cfg +0 -0
  66. {spacr-0.2.3 → spacr-0.2.5}/spacr/__init__.py +0 -0
  67. {spacr-0.2.3 → spacr-0.2.5}/spacr/__main__.py +0 -0
  68. {spacr-0.2.3 → spacr-0.2.5}/spacr/app_classify.py +0 -0
  69. {spacr-0.2.3 → spacr-0.2.5}/spacr/app_make_masks.py +0 -0
  70. {spacr-0.2.3 → spacr-0.2.5}/spacr/app_mask.py +0 -0
  71. {spacr-0.2.3 → spacr-0.2.5}/spacr/app_measure.py +0 -0
  72. {spacr-0.2.3 → spacr-0.2.5}/spacr/app_sequencing.py +0 -0
  73. {spacr-0.2.3 → spacr-0.2.5}/spacr/app_umap.py +0 -0
  74. {spacr-0.2.3 → spacr-0.2.5}/spacr/chris.py +0 -0
  75. {spacr-0.2.3 → spacr-0.2.5}/spacr/deep_spacr.py +0 -0
  76. {spacr-0.2.3 → spacr-0.2.5}/spacr/graph_learning.py +0 -0
  77. {spacr-0.2.3 → spacr-0.2.5}/spacr/logger.py +0 -0
  78. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/abort.png +0 -0
  79. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/annotate.png +0 -0
  80. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/cellpose_all.png +0 -0
  81. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/cellpose_masks.png +0 -0
  82. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/classify.png +0 -0
  83. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/default.png +0 -0
  84. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/download.png +0 -0
  85. /spacr-0.2.3/spacr/resources/icons/logo_spacr.png → /spacr-0.2.5/spacr/resources/icons/logo_spacr_1.png +0 -0
  86. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/make_masks.png +0 -0
  87. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/map_barcodes.png +0 -0
  88. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/mask.png +0 -0
  89. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/measure.png +0 -0
  90. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/ml_analyze.png +0 -0
  91. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/recruitment.png +0 -0
  92. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/regression.png +0 -0
  93. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/run.png +0 -0
  94. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/sequencing.png +0 -0
  95. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/settings.png +0 -0
  96. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/spacr_logo_rotation.gif +0 -0
  97. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/train_cellpose.png +0 -0
  98. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/umap.png +0 -0
  99. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model +0 -0
  100. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv +0 -0
  101. {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/models/cp/toxo_pv_lumen.CP_model +0 -0
  102. {spacr-0.2.3 → spacr-0.2.5}/spacr/sequencing.py +0 -0
  103. {spacr-0.2.3 → spacr-0.2.5}/spacr/sim.py +0 -0
  104. {spacr-0.2.3 → spacr-0.2.5}/spacr/sim_app.py +0 -0
  105. {spacr-0.2.3 → spacr-0.2.5}/spacr/timelapse.py +0 -0
  106. {spacr-0.2.3 → spacr-0.2.5}/spacr/version.py +0 -0
  107. {spacr-0.2.3 → spacr-0.2.5}/spacr.egg-info/dependency_links.txt +0 -0
  108. {spacr-0.2.3 → spacr-0.2.5}/spacr.egg-info/entry_points.txt +0 -0
  109. {spacr-0.2.3 → spacr-0.2.5}/spacr.egg-info/top_level.txt +0 -0
  110. {spacr-0.2.3 → spacr-0.2.5}/tests/test_annotate_app.py +0 -0
  111. {spacr-0.2.3 → spacr-0.2.5}/tests/test_core.py +0 -0
  112. {spacr-0.2.3 → spacr-0.2.5}/tests/test_gui_classify_app.py +0 -0
  113. {spacr-0.2.3 → spacr-0.2.5}/tests/test_gui_mask_app.py +0 -0
  114. {spacr-0.2.3 → spacr-0.2.5}/tests/test_gui_measure_app.py +0 -0
  115. {spacr-0.2.3 → spacr-0.2.5}/tests/test_gui_sim_app.py +0 -0
  116. {spacr-0.2.3 → spacr-0.2.5}/tests/test_gui_utils.py +0 -0
  117. {spacr-0.2.3 → spacr-0.2.5}/tests/test_io.py +0 -0
  118. {spacr-0.2.3 → spacr-0.2.5}/tests/test_mask_app.py +0 -0
  119. {spacr-0.2.3 → spacr-0.2.5}/tests/test_measure.py +0 -0
  120. {spacr-0.2.3 → spacr-0.2.5}/tests/test_plot.py +0 -0
  121. {spacr-0.2.3 → spacr-0.2.5}/tests/test_sim.py +0 -0
  122. {spacr-0.2.3 → spacr-0.2.5}/tests/test_timelapse.py +0 -0
  123. {spacr-0.2.3 → spacr-0.2.5}/tests/test_train.py +0 -0
  124. {spacr-0.2.3 → spacr-0.2.5}/tests/test_umap.py +0 -0
  125. {spacr-0.2.3 → spacr-0.2.5}/tests/test_utils.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: spacr
3
- Version: 0.2.3
3
+ Version: 0.2.5
4
4
  Summary: Spatial phenotype analysis of crisp screens (SpaCr)
5
5
  Home-page: https://github.com/EinarOlafsson/spacr
6
6
  Author: Einar Birnir Olafsson
@@ -39,6 +39,10 @@ Requires-Dist: ttf_opensans>=2020.10.30
39
39
  Requires-Dist: customtkinter<6.0,>=5.2.2
40
40
  Requires-Dist: biopython<2.0,>=1.80
41
41
  Requires-Dist: lxml<6.0,>=5.1.0
42
+ Requires-Dist: psutil<6.0,>=5.9.8
43
+ Requires-Dist: gputil<2.0,>=1.4.0
44
+ Requires-Dist: gpustat<2.0,>=1.1.1
45
+ Requires-Dist: pyautogui<1.0,>=0.9.54
42
46
  Requires-Dist: huggingface-hub<0.25,>=0.24.0
43
47
  Provides-Extra: dev
44
48
  Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
@@ -45,12 +45,16 @@ dependencies = [
45
45
  'customtkinter>=5.2.2,<6.0',
46
46
  'biopython>=1.80,<2.0',
47
47
  'lxml>=5.1.0,<6.0',
48
+ 'psutil>=5.9.8, <6.0',
49
+ 'gputil>=1.4.0, <2.0',
50
+ 'gpustat>=1.1.1,<2.0',
51
+ 'pyautogui>=0.9.54,<1.0',
48
52
  'huggingface-hub>=0.24.0,<0.25'
49
53
  ]
50
54
 
51
55
  setup(
52
56
  name="spacr",
53
- version="0.2.3",
57
+ version="0.2.5",
54
58
  author="Einar Birnir Olafsson",
55
59
  author_email="olafsson@med.umich.com",
56
60
  description="Spatial phenotype analysis of crisp screens (SpaCr)",
@@ -58,7 +62,7 @@ setup(
58
62
  url="https://github.com/EinarOlafsson/spacr",
59
63
  packages=find_packages(exclude=["tests.*", "tests"]),
60
64
  include_package_data=True,
61
- package_data={'spacr': ['resources/models/cp/*', 'resources/icons/*'],},
65
+ package_data={'spacr': ['resources/models/cp/*', 'resources/icons/*', 'resources/font/**/*'],},
62
66
  install_requires=dependencies,
63
67
  entry_points={
64
68
  'console_scripts': [
@@ -1,7 +1,7 @@
1
1
  import tkinter as tk
2
2
  from tkinter import ttk
3
3
  from .gui import MainApp
4
- from .gui_elements import set_dark_style
4
+ from .gui_elements import set_dark_style, spacrButton
5
5
 
6
6
  def initiate_annotation_app(parent_frame):
7
7
  from .gui_utils import generate_annotate_fields, annotate_app
@@ -20,8 +20,6 @@ def initiate_annotation_app(parent_frame):
20
20
  settings['img_size'] = list(map(int, settings['img_size'].split(','))) # Convert string to list of integers
21
21
  settings['percentiles'] = list(map(int, settings['percentiles'].split(','))) # Convert string to list of integers
22
22
  settings['normalize'] = settings['normalize'].lower() == 'true'
23
- settings['rows'] = int(settings['rows'])
24
- settings['columns'] = int(settings['columns'])
25
23
 
26
24
  try:
27
25
  settings['measurement'] = settings['measurement'].split(',') if settings['measurement'] else None
@@ -40,9 +38,10 @@ def initiate_annotation_app(parent_frame):
40
38
  settings[key] = None
41
39
 
42
40
  settings_window.destroy()
41
+
43
42
  annotate_app(parent_frame, settings)
44
43
 
45
- start_button = tk.Button(settings_window, text="Start Annotation", command=start_annotation_app, bg=style_out['bg_color'], fg=style_out['bg_color'])
44
+ start_button = spacrButton(settings_window, text="annotate", command=start_annotation_app, show_text=False)
46
45
  start_button.pack(pady=10)
47
46
 
48
47
  def start_annotate_app():