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.
- {spacr-0.2.3/spacr.egg-info → spacr-0.2.5}/PKG-INFO +5 -1
- {spacr-0.2.3 → spacr-0.2.5}/setup.py +6 -2
- {spacr-0.2.3 → spacr-0.2.5}/spacr/app_annotate.py +3 -4
- {spacr-0.2.3 → spacr-0.2.5}/spacr/core.py +100 -282
- {spacr-0.2.3 → spacr-0.2.5}/spacr/gui.py +20 -38
- spacr-0.2.5/spacr/gui_core.py +696 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/gui_elements.py +395 -60
- spacr-0.2.5/spacr/gui_utils.py +640 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/io.py +130 -50
- {spacr-0.2.3 → spacr-0.2.5}/spacr/measure.py +199 -154
- {spacr-0.2.3 → spacr-0.2.5}/spacr/plot.py +108 -42
- spacr-0.2.5/spacr/resources/font/open_sans/OFL.txt +93 -0
- spacr-0.2.5/spacr/resources/font/open_sans/OpenSans-Italic-VariableFont_wdth,wght.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/OpenSans-VariableFont_wdth,wght.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/README.txt +100 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-Bold.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-BoldItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-ExtraBold.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-ExtraBoldItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-Italic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-Light.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-LightItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-Medium.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-MediumItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-Regular.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-SemiBold.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans-SemiBoldItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-Bold.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-BoldItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-ExtraBold.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-ExtraBoldItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-Italic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-Light.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-LightItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-Medium.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-MediumItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-Regular.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-SemiBold.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_Condensed-SemiBoldItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Bold.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-BoldItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-ExtraBold.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-ExtraBoldItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Italic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Light.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-LightItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Medium.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-MediumItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Regular.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-SemiBold.ttf +0 -0
- spacr-0.2.5/spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-SemiBoldItalic.ttf +0 -0
- spacr-0.2.5/spacr/resources/icons/logo.pdf +2786 -6
- spacr-0.2.5/spacr/resources/icons/logo_spacr.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/settings.py +12 -87
- {spacr-0.2.3 → spacr-0.2.5}/spacr/utils.py +45 -10
- {spacr-0.2.3 → spacr-0.2.5/spacr.egg-info}/PKG-INFO +5 -1
- spacr-0.2.5/spacr.egg-info/SOURCES.txt +120 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr.egg-info/requires.txt +4 -0
- spacr-0.2.3/spacr/gui_core.py +0 -789
- spacr-0.2.3/spacr/gui_utils.py +0 -320
- spacr-0.2.3/spacr.egg-info/SOURCES.txt +0 -78
- {spacr-0.2.3 → spacr-0.2.5}/LICENSE +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/MANIFEST.in +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/README.rst +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/setup.cfg +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/__init__.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/__main__.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/app_classify.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/app_make_masks.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/app_mask.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/app_measure.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/app_sequencing.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/app_umap.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/chris.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/deep_spacr.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/graph_learning.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/logger.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/abort.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/annotate.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/cellpose_all.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/cellpose_masks.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/classify.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/default.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/download.png +0 -0
- /spacr-0.2.3/spacr/resources/icons/logo_spacr.png → /spacr-0.2.5/spacr/resources/icons/logo_spacr_1.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/make_masks.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/map_barcodes.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/mask.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/measure.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/ml_analyze.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/recruitment.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/regression.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/run.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/sequencing.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/settings.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/spacr_logo_rotation.gif +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/train_cellpose.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/icons/umap.png +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/resources/models/cp/toxo_pv_lumen.CP_model +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/sequencing.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/sim.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/sim_app.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/timelapse.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr/version.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr.egg-info/dependency_links.txt +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr.egg-info/entry_points.txt +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/spacr.egg-info/top_level.txt +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_annotate_app.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_core.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_gui_classify_app.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_gui_mask_app.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_gui_measure_app.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_gui_sim_app.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_gui_utils.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_io.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_mask_app.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_measure.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_plot.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_sim.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_timelapse.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_train.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_umap.py +0 -0
- {spacr-0.2.3 → spacr-0.2.5}/tests/test_utils.py +0 -0
@@ -1,6 +1,6 @@
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Metadata-Version: 2.1
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Name: spacr
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Version: 0.2.
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Version: 0.2.5
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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
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Requires-Dist: customtkinter<6.0,>=5.2.2
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Requires-Dist: biopython<2.0,>=1.80
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Requires-Dist: lxml<6.0,>=5.1.0
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Requires-Dist: psutil<6.0,>=5.9.8
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Requires-Dist: gputil<2.0,>=1.4.0
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Requires-Dist: gpustat<2.0,>=1.1.1
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Requires-Dist: pyautogui<1.0,>=0.9.54
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Requires-Dist: huggingface-hub<0.25,>=0.24.0
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Provides-Extra: dev
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Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
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'customtkinter>=5.2.2,<6.0',
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'biopython>=1.80,<2.0',
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'lxml>=5.1.0,<6.0',
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'psutil>=5.9.8, <6.0',
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'gputil>=1.4.0, <2.0',
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'gpustat>=1.1.1,<2.0',
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'pyautogui>=0.9.54,<1.0',
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'huggingface-hub>=0.24.0,<0.25'
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]
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setup(
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name="spacr",
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version="0.2.
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version="0.2.5",
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author="Einar Birnir Olafsson",
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author_email="olafsson@med.umich.com",
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description="Spatial phenotype analysis of crisp screens (SpaCr)",
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url="https://github.com/EinarOlafsson/spacr",
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packages=find_packages(exclude=["tests.*", "tests"]),
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include_package_data=True,
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package_data={'spacr': ['resources/models/cp/*', 'resources/icons/*'],},
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package_data={'spacr': ['resources/models/cp/*', 'resources/icons/*', 'resources/font/**/*'],},
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install_requires=dependencies,
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entry_points={
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'console_scripts': [
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import tkinter as tk
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from tkinter import ttk
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from .gui import MainApp
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from .gui_elements import set_dark_style, spacrButton
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def initiate_annotation_app(parent_frame):
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from .gui_utils import generate_annotate_fields, annotate_app
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settings['img_size'] = list(map(int, settings['img_size'].split(','))) # Convert string to list of integers
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settings['percentiles'] = list(map(int, settings['percentiles'].split(','))) # Convert string to list of integers
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settings['normalize'] = settings['normalize'].lower() == 'true'
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try:
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settings['measurement'] = settings['measurement'].split(',') if settings['measurement'] else None
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annotate_app(parent_frame, settings)
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start_button =
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start_button = spacrButton(settings_window, text="annotate", command=start_annotation_app, show_text=False)
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start_button.pack(pady=10)
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def start_annotate_app():
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