spacr 0.2.32__py3-none-any.whl → 0.2.45__py3-none-any.whl

spacr/settings.py

@@ -1114,7 +1114,7 @@ categories = {
 }
 
 descriptions = {
-    'mask': "Generate Cellpose masks for Cells, Nuclei, and Pathogens. Function: preprocess_generate_masks from spacr.core.\n\nKey Features:\n- Automated Mask Generation: Automatically generate accurate masks for various cellular components using Cellpose, a robust deep learning model for cell segmentation.\n- Versatility: Capable of handling different types of biological samples, including cells, nuclei, and pathogens.\n- Integration: Directly integrates with other modules, providing the foundational masks required for subsequent analysis.",
+    'mask': "\n\nHelp:\n- Generate Cells, Nuclei, Pathogens, and Cytoplasm masks from intensity images in src.\n- To ensure that spacr is installed correctly:\n- 1. Downloade the training set (click Download).\n- 2. Import settings (click settings navigate to downloaded dataset settings folder and import preprocess_generate_masks_settings.csv).\n- 3. Run the module.\n- 4. Proceed to the Measure module (click Measure in the menue bar).\n- For further help, click the Help button in the menue bar.",
     
     'measure': "Capture Measurements from Cells, Nuclei, Pathogens, and Cytoplasm objects. Generate single object PNG images for one or several objects. (Requires masks from the Mask module). Function: measure_crop from spacr.measure.\n\nKey Features:\n- Comprehensive Measurement Capture: Obtain detailed measurements for various cellular components, including area, perimeter, intensity, and more.\n- Image Generation: Create high-resolution PNG images of individual objects, facilitating further analysis and visualization.\n- Mask Dependency: Requires accurate masks generated by the Mask module to ensure precise measurements.",
     

spacr/utils.py

@@ -87,27 +87,6 @@ from scipy.stats import f_oneway, kruskal
 from sklearn.cluster import KMeans
 from scipy import stats
 
-def print_progress_v1(files_processed, files_to_process, n_jobs, time_ls=None, batch_size=None, operation_type=""):
-    if isinstance(files_processed, list):
-        files_processed = len(files_processed)
-    if isinstance(files_to_process, list):
-        files_to_process = len(files_to_process)
-    if isinstance(batch_size, list):
-        batch_size = len(batch_size)
-
-    if time_ls is not None:
-        average_time = np.mean(time_ls) if len(time_ls) > 0 else 0
-        time_left = (((files_to_process-files_processed)*average_time)/n_jobs)/60
-        if batch_size is None:
-            print(f'Time/image: {average_time:.3f}sec')
-            print(f'Time_left: {time_left:.3f} min.')
-        else:
-            average_time_img = average_time/batch_size
-            print(f'Time/batch:{average_time:.3f}sec')
-            print(f'Time/image {average_time_img:.3f}')
-            print(f'Time_left: {time_left:.3f} min.')
-            
-    print(f'Progress: {files_processed}/{files_to_process}, operation_type: {operation_type}')
 
 def print_progress(files_processed, files_to_process, n_jobs, time_ls=None, batch_size=None, operation_type=""):
     if isinstance(files_processed, list):
@@ -2989,11 +2968,13 @@ def _choose_model(model_name, device, object_type='cell', restore_type=None, obj
     if restore_type == None:
         if model_name in ['cyto', 'cyto2', 'cyto3', 'nuclei']:
             model = cp_models.Cellpose(gpu=torch.cuda.is_available(), model_type=model_name, device=device)
-
+            return model
     else:
         if object_type == 'nucleus':
             restore = f'{type}_nuclei'
             model = denoise.CellposeDenoiseModel(gpu=torch.cuda.is_available(), model_type="nuclei",restore_type=restore, chan2_restore=False, device=device)
+            return model
+
         else:
             restore = f'{type}_cyto3'
             if model_name =='cyto2':
@@ -3001,8 +2982,7 @@ def _choose_model(model_name, device, object_type='cell', restore_type=None, obj
             if model_name =='cyto':
                 chan2_restore = False
             model = denoise.CellposeDenoiseModel(gpu=torch.cuda.is_available(), model_type="cyto3",restore_type=restore, chan2_restore=chan2_restore, device=device)
-    
-    return model
+            return model
 
 class SelectChannels:
     def __init__(self, channels):

{spacr-0.2.32.dist-info → spacr-0.2.45.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.32
+Version: 0.2.45
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -39,6 +39,9 @@ Requires-Dist: ttf-opensans >=2020.10.30
 Requires-Dist: customtkinter <6.0,>=5.2.2
 Requires-Dist: biopython <2.0,>=1.80
 Requires-Dist: lxml <6.0,>=5.1.0
+Requires-Dist: psutil <6.0,>=5.9.8
+Requires-Dist: gputil <2.0,>=1.4.0
+Requires-Dist: gpustat <2.0,>=1.1.1
 Requires-Dist: huggingface-hub <0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest <3.11,>=3.9 ; extra == 'dev'

{spacr-0.2.32.dist-info → spacr-0.2.45.dist-info}/RECORD

@@ -8,23 +8,23 @@ spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
 spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
 spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
-spacr/core.py,sha256=iAH6de2dW0nKVtVeBjdWOhSW_KoHlVDVOoOsHb6vGC0,148884
+spacr/core.py,sha256=aAVL5E2Dg7LA16UBoEJsR9jHVJ1-lMJBIwNsfv6hVQ4,148385
 spacr/deep_spacr.py,sha256=ASBsN4JpHp_3S-91JUsB34IWTjTGPYI7jKV2qZnUR5M,37005
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
-spacr/gui.py,sha256=bA1Qy6D9aeL_Qe0Xeql8bRkbbFajAMGTZZR3uBzIW1Q,8495
-spacr/gui_core.py,sha256=4II8TscaDHDvRXc4D-azQyAeVGNkqyN6_HaNhkjij4s,35546
-spacr/gui_elements.py,sha256=X04aSf2WGIZ3JqdJMD26hKOgyJ4hOdTfyUrb-NttiyY,96208
-spacr/gui_utils.py,sha256=ySSDDYmY80h_Wk2Nb1oxbugRU2TWt6N7BwusUl_-wRo,14970
-spacr/io.py,sha256=Dehuqn_oGo0gcyezQIw9rUUvO7oOHDWuMkPDSCgyrp8,115521
+spacr/gui.py,sha256=NoqaHYjqvyiexfXMsFWrRYjcyqAOhEIYnR-82LkKzdk,7277
+spacr/gui_core.py,sha256=7Dmm_KGYwCHpm_n5pz5M1OVj6RxdznG21jriGHpj6c4,31894
+spacr/gui_elements.py,sha256=vxgsCaF_YkvTieliJkHLDZjGnH79vS8vOixdYhElhf4,102043
+spacr/gui_utils.py,sha256=-SOVMToUhbrNpvsaZkrBkBKE9YOU3fJqlkpoxQKnPPY,26221
+spacr/io.py,sha256=AnQn-iS8SZpGJ4EOQ14MYkjvE_MGw1Uy9VBRJrHKnqc,115084
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
-spacr/measure.py,sha256=W5_yuLnsFSafuZNcKzVsCTJSTfpbNgrGTuxG1OVb0iU,55283
-spacr/plot.py,sha256=DYJEoK1kz2ih6ZGvKiA3xTqeIeKQNhuQKwgrscopFxA,69101
+spacr/measure.py,sha256=u7j3z8wJyDQt24vh0nUmrI7uS1hei_9p_zlmAwoT4zI,55295
+spacr/plot.py,sha256=ihyseFapQuF1JPzno2FaTpltgFYZZjTdrF56s5mYbQ8,73626
 spacr/sequencing.py,sha256=fHZRnoMSxmhMdadkei3lUeBdckqFyptWdQyWsDW3aaU,83304
-spacr/settings.py,sha256=deX0pNwTqyHojpCTiF060RSK5oPeSEcS_s6UlVc0x3Q,65442
+spacr/settings.py,sha256=Js1-CwR8It9DKIfikfpt0GXpFNJN08udyGLaHZ6IMnE,65395
 spacr/sim.py,sha256=FveaVgBi3eypO2oVB5Dx-v0CC1Ny7UPfXkJiiRRodAk,71212
 spacr/sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 spacr/timelapse.py,sha256=KMYCgHzf9LTZe-lWl5mvH2EjbKRE6OhpwdY13wEumGc,39504
-spacr/utils.py,sha256=r23Cd94HT3q1kMIbyEmyvJVnnDOY16plvUXVwxuX1PE,189256
+spacr/utils.py,sha256=_aIhV_2frswNZCVXgPOJeO1Pfm_WbdOEhd8phWLKkII,188277
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/icons/abort.png,sha256=avtIRT7aCJsdZ1WnY_rZStm6cCji5bYPLnlptdcTNcM,6583
 spacr/resources/icons/annotate.png,sha256=GFgh7DiUMwPG_-xE6W1qU8V_qzSwBi1xKenfoaQxeFA,15495
@@ -33,7 +33,9 @@ spacr/resources/icons/cellpose_masks.png,sha256=HVWOIOBF8p3-On-2UahwMyQXp7awsoC5
 spacr/resources/icons/classify.png,sha256=-iv4sqAwUVJO3CG6fHKHf3_BB0s-I2i4prg-iR7dSBM,35897
 spacr/resources/icons/default.png,sha256=KoNhaSHukO4wDyivyYEgSbb5mGj-sAxmhKikLLtNpWs,20341
 spacr/resources/icons/download.png,sha256=1nUoWRaTc4vIsK6gompdeqk0cIv2GdH-gCNHaEBX6Mc,20467
-spacr/resources/icons/logo_spacr.png,sha256=g9y2ZmnV3hab8r1idDfytm8AaHbBiQdu_93Jd7YKzwA,610892
+spacr/resources/icons/logo.pdf,sha256=VB4cS41V3VV_QxD7l6CwdQKQiYLErugLBxWoCoxjQU0,377925
+spacr/resources/icons/logo_spacr.png,sha256=qG3e3bdrAefhl1281rfo0R2XP0qA-c-oaBCXjxMGXkw,42587
+spacr/resources/icons/logo_spacr_1.png,sha256=g9y2ZmnV3hab8r1idDfytm8AaHbBiQdu_93Jd7YKzwA,610892
 spacr/resources/icons/make_masks.png,sha256=iB4kaTgbgyygSJSNstVKhRIXKSgWYkeh7Gt3ox-kWDI,42493
 spacr/resources/icons/map_barcodes.png,sha256=ED6yCopk3hP7tICSvT8U_qA1bOOb0WHqmxVkmRxnbtE,7896
 spacr/resources/icons/mask.png,sha256=DcBes-3UJ7XjRfj_P4RttRp680ZKZeH9a-DSk7bIF5U,37658
@@ -50,9 +52,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model,sha256=z8BbHWZPRnE9D_BHO0fBREE85c1vkltDs-incs2ytXQ,26566572
 spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv,sha256=fBAGuL_B8ERVdVizO3BHozTDSbZUh1yFzsYK3wkQN68,420
 spacr/resources/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.2.32.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.2.32.dist-info/METADATA,sha256=7GPY-yVzmB8pnDA1LszwCL7ls2OEQUcKla_s6br0ncc,5050
-spacr-0.2.32.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.2.32.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.2.32.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.2.32.dist-info/RECORD,,
+spacr-0.2.45.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.2.45.dist-info/METADATA,sha256=NCoOOcQM14mXWrbWCe8o64hNgWYn4fl1AaDhHJXiwWE,5156
+spacr-0.2.45.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.2.45.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.2.45.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.2.45.dist-info/RECORD,,