spacr 0.1.12__py3-none-any.whl → 0.1.50__py3-none-any.whl

spacr/measure.py

@@ -617,6 +617,13 @@ def _measure_crop_core(index, time_ls, file, settings):
     start = time.time() 
     try:
         source_folder = os.path.dirname(settings['input_folder'])
+        #if not os.path.basename(source_folder).endswith('merged'):
+        #    source_folder = os.path.join(source_folder, 'merged')
+        #    print(f'changed source_folder to {source_folder}')
+
+        #if not os.path.exists(source_folder):
+        #    return
+
         file_name = os.path.splitext(file)[0]
         data = np.load(os.path.join(settings['input_folder'], file))
 
@@ -750,6 +757,15 @@ def _measure_crop_core(index, time_ls, file, settings):
             if isinstance(settings['crop_mode'], list):
                 crop_ls = settings['crop_mode']
                 size_ls = settings['png_size']
+                
+                if isinstance(size_ls[0], int):
+                    size_ls = [size_ls]
+                if len(crop_ls) > 1 and len(size_ls) == 1:
+                    size_ls = size_ls * len(crop_ls)
+                    
+                if len(crop_ls) != len(size_ls):
+                    print(f"Setting: size_ls: {settings['png_size']} should be a list of integers, or a list of lists of integers if crop_ls: {settings['crop_mode']} has multiple elements")
+                    
                 for crop_idx, crop_mode in enumerate(crop_ls):
                     width, height = size_ls[crop_idx]
                     if crop_mode == 'cell':
@@ -926,9 +942,14 @@ def measure_crop(settings):
     settings = get_measure_crop_settings(settings)
     settings = measure_test_mode(settings)
 
-    if not os.path.exists(settings['input_folder']):
-        print(f"Error: {settings['input_folder']} does not exist")
-        return
+    #src_fldr = settings['input_folder']
+    #if not os.path.basename(src_fldr).endswith('merged'):
+    #    settings['input_folder'] = os.path.join(src_fldr, 'merged')
+    #    print(f"changed input_folder to {src_fldr}")
+
+    #if not os.path.exists(settings['input_folder']):
+    #    print(f'input_folder: {settings["input_folder"]} does not exist')
+    #    return
     
     if settings['cell_mask_dim'] is None:
         settings['include_uninfected'] = True

spacr/settings.py

@@ -27,7 +27,13 @@ def set_default_plot_merge_settings():
 
 def set_default_settings_preprocess_generate_masks(src, settings={}):
     # Main settings
-    settings['src'] = src
+    if src != None:
+        settings['src'] = src
+    else:
+        settings.setdefault('src', 'path')
+    if 'src' not in settings:
+        settings['src'] = 'path'
+
     settings.setdefault('preprocess', True)
     settings.setdefault('masks', True)
     settings.setdefault('save', True)
@@ -212,9 +218,12 @@ def get_umap_image_settings(settings={}):
 
 def get_measure_crop_settings(settings):
 
+    settings.setdefault('src', 'path')
+    
     # Test mode
     settings.setdefault('test_mode', False)
     settings.setdefault('test_nr', 10)
+    settings.setdefault('channels', [0,1,2,3])
 
     #measurement settings
     settings.setdefault('save_measurements',True)
@@ -260,7 +269,7 @@ def get_measure_crop_settings(settings):
 
     # Miscellaneous settings
     settings.setdefault('experiment', 'exp')
-    settings.setdefault('cells', 'HeLa')
+    settings.setdefault('cells', ['HeLa'])
     settings.setdefault('cell_loc', None)
     settings.setdefault('pathogens', ['ME49Dku80WT', 'ME49Dku80dgra8:GRA8', 'ME49Dku80dgra8', 'ME49Dku80TKO'])
     settings.setdefault('pathogen_loc', [['c1', 'c2', 'c3', 'c4', 'c5', 'c6'], ['c7', 'c8', 'c9', 'c10', 'c11', 'c12'], ['c13', 'c14', 'c15', 'c16', 'c17', 'c18'], ['c19', 'c20', 'c21', 'c22', 'c23', 'c24']])
@@ -304,6 +313,8 @@ def set_default_analyze_screen(settings):
 
 def set_default_train_test_model(settings):
     cores = os.cpu_count()-2
+
+    settings.setdefault('src','path')
     settings.setdefault('train',True)
     settings.setdefault('test',False)
     settings.setdefault('classes',['nc','pc'])

spacr/utils.py

@@ -73,6 +73,65 @@ from scipy import stats
 
 from .logger import log_function_call
 
+import os
+import signal
+import psutil
+import platform
+from multiprocessing import set_start_method, get_start_method
+
+def reset_mp():
+    current_method = get_start_method()
+    system = platform.system()
+    
+    if system == 'Windows':
+        if current_method != 'spawn':
+            set_start_method('spawn', force=True)
+    elif system in ('Linux', 'Darwin'):  # Darwin is macOS
+        if current_method != 'fork':
+            set_start_method('fork', force=True)
+
+def is_multiprocessing_process(process):
+    """ Check if the process is a multiprocessing process. """
+    try:
+        for cmd in process.cmdline():
+            if 'multiprocessing' in cmd:
+                return True
+    except (psutil.NoSuchProcess, psutil.AccessDenied, psutil.ZombieProcess):
+        pass
+    return False
+
+def close_file_descriptors():
+    """ Close file descriptors and shared memory objects. """
+    import resource
+
+    soft, hard = resource.getrlimit(resource.RLIMIT_NOFILE)
+    for fd in range(3, soft):
+        try:
+            os.close(fd)
+        except OSError:
+            pass
+
+def close_multiprocessing_processes():
+    """ Close all multiprocessing processes. """
+    current_pid = os.getpid()
+    for proc in psutil.process_iter(['pid', 'cmdline']):
+        try:
+            # Skip the current process
+            if proc.info['pid'] == current_pid:
+                continue
+            
+            # Check if the process is a multiprocessing process
+            if is_multiprocessing_process(proc):
+                proc.terminate()
+                proc.wait(timeout=5)  # Wait up to 5 seconds for the process to terminate
+                print(f"Terminated process {proc.info['pid']}")
+        
+        except (psutil.NoSuchProcess, psutil.AccessDenied, psutil.ZombieProcess) as e:
+            print(f"Failed to terminate process {proc.info['pid']}: {e}")
+
+    # Close file descriptors
+    close_file_descriptors()
+
 def check_mask_folder(src,mask_fldr):
     
     mask_folder = os.path.join(src,'norm_channel_stack',mask_fldr)
@@ -92,19 +151,14 @@ def check_mask_folder(src,mask_fldr):
 
 def smooth_hull_lines(cluster_data):
     hull = ConvexHull(cluster_data)
-
     # Extract vertices of the hull
     vertices = hull.points[hull.vertices]
-
     # Close the loop
     vertices = np.vstack([vertices, vertices[0, :]])
-
     # Parameterize the vertices
     tck, u = splprep(vertices.T, u=None, s=0.0)
-
     # Evaluate spline at new parameter values
     new_points = splev(np.linspace(0, 1, 100), tck)
-
     return new_points[0], new_points[1]
 
 def _gen_rgb_image(image, channels):

{spacr-0.1.12.dist-info → spacr-0.1.50.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.12
+Version: 0.1.50
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -9,7 +9,6 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
-Requires-Dist: dgl ==0.9.1
 Requires-Dist: torch <3.0,>=2.2.1
 Requires-Dist: torchvision <1.0,>=0.17.1
 Requires-Dist: torch-geometric <3.0,>=2.5.1
@@ -40,12 +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: qtpy <2.5,>=2.4.1
-Requires-Dist: superqt <0.7,>=0.6.7
-Requires-Dist: pyqt6 <6.8,>=6.7.1
-Requires-Dist: pyqtgraph <0.14,>=0.13.7
+Requires-Dist: huggingface-hub <0.25,>=0.24.0
 Provides-Extra: dev
-Requires-Dist: pytest >=3.9 ; extra == 'dev'
+Requires-Dist: pytest <3.11,>=3.9 ; extra == 'dev'
 Provides-Extra: full
 Requires-Dist: opencv-python ; extra == 'full'
 Provides-Extra: headless
@@ -67,7 +63,7 @@ Requires-Dist: opencv-python-headless ; extra == 'headless'
 SpaCr
 =====
 
-Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understand host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
+Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understanding host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
 
 Features
 --------
@@ -76,9 +72,9 @@ Features
 
 -  **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
 
--  **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 a SQL database that can be annotated and used to train CNNs/Transformer models for classification tasks.
+-  **Crop Images:** Save objects (cells, nuclei, pathogen, cytoplasm) as images. Object image paths are saved in a SQL database.
 
--  **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
+-  **Train CNNs or Transformers:** Train Torch models to classify single object images.
 
 -  **Manual Annotation:** Supports manual annotation of single-cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
 
@@ -95,29 +91,20 @@ Features
 Installation
 ------------
 
-Requires Tkinter for graphical user interface features.
+If using Windows, switch to Linux—it's free, open-source, and better.
 
-Ubuntu
-~~~~~~
+Before installing SpaCr on OSX ensure OpenMP is installed::
 
-Before installing SpaCr, ensure Tkinter is installed:
+   brew install libomp
 
-(Tkinter is included with the standard Python installation on macOS, and Windows)
-
-On Linux:
-
-::
+SpaCr GUI requires Tkinter. On Linux, ensure Tkinter is installed. (Tkinter is included with the standard Python installation on macOS and Windows)::
 
    sudo apt-get install python3-tk
 
-Install spacr with pip
-
-::
+Install SpaCr with pip::
 
    pip install spacr
 
-Run spacr GUI:
-
-::
+Run SpaCr GUI::
 
-   gui
+   spacr

{spacr-0.1.12.dist-info → spacr-0.1.50.dist-info}/RECORD

@@ -3,21 +3,21 @@ spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
 spacr/alpha.py,sha256=Y95sLEfpK2OSYKRn3M8eUOU33JJeXfV8zhrC4KnwSTY,35244
 spacr/annotate_app.py,sha256=imQ7ZEXDyM6ce1dxZ1xUS1-KequuF_NCI4xCaPLjvco,29275
 spacr/annotate_app_v2.py,sha256=imQ7ZEXDyM6ce1dxZ1xUS1-KequuF_NCI4xCaPLjvco,29275
-spacr/app_annotate.py,sha256=I0c-Q5WYkA2lCKyNByACM1YzSdLC17X2mNJ2XAnWgNQ,23619
-spacr/app_classify.py,sha256=052t5MeUsP6IdJTA_uWY4AmyBHTkf8_KdslfDWtP7pk,8428
-spacr/app_make_masks.py,sha256=fIlWG13PMrafvwj92el1Puo48CJy4Q3iINOXa5mW3oI,45136
-spacr/app_make_masks_v2.py,sha256=-HhEgi0ber1Jyjp5RgqUcZM4vPvGXPKh1pv3SLyVZoU,30574
-spacr/app_mask.py,sha256=kp0Zvw9uA-Z8FfuKChrXo1DA01_H7fdKCsFZzmKKrtI,10731
-spacr/app_measure.py,sha256=85ux3Udw0GRjr7h2XoID752wvQCTtdHsfFSQOwWOkV0,10623
+spacr/app_annotate.py,sha256=vL4u_54bOZ2BO-azEgMG9HlNBXBLCzhIs10QggS6Adk,23572
+spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
+spacr/app_make_masks.py,sha256=rV2zoxYsJ8-uR39mXjDMkbNcxv-6vq2POw4QUTDD8_U,45072
+spacr/app_make_masks_v2.py,sha256=jmLYKJSPhI3Zf5MnbHqLNO2asI49a0BBOo2Y4p2uz4o,30528
+spacr/app_mask.py,sha256=l-dBY8ftzCMdDe6-pXc2Nh_u-idNL9G7UOARiLJBtds,153
+spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
 spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
 spacr/classify_app.py,sha256=Zi15ryc1ocYitRF4kyxlC27XxGyzfSPdvj2d6ZrSh7E,8446
 spacr/cli.py,sha256=507jfOOEV8BoL4eeUcblvH-iiDHdBrEVJLu1ghAAPSc,1800
 spacr/core.py,sha256=m9fsk-qDPow4AzOYpTIsd4jT7PF_L_4y5xillR5eRdk,160253
-spacr/deep_spacr.py,sha256=N0o7ILD2p1FTfU4DFxnpjs00xjLhwib-ev0XGqA6muU,37035
+spacr/deep_spacr.py,sha256=rvqOoY9dadcTcKiABf61Nb8HEMVp1NouFmtAE2ee1T4,37056
 spacr/foldseek.py,sha256=YIP1d4Ci6CeA9jSyiv-HTDbNmAmcSM9Y_DaOs7wYzLY,33546
 spacr/get_alfafold_structures.py,sha256=ehx_MQgb12k3hFecP6cYVlm5TLO8iWjgevy8ESyS3cw,3544
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
-spacr/gui.py,sha256=nwRqK3DLYrJQh4iCoyfJMpwSuxCn1xc4zHLmQ8cW8Is,6519
+spacr/gui.py,sha256=1pumw2O0dfDZ4Hw4V8-pMlvODegDNulXsLNEFAnIB7c,7297
 spacr/gui_2.py,sha256=ZAI5quQYbhQJ40vK0NCqU_UMSPLkpfeQpomBWUSM0fc,6946
 spacr/gui_annotate.py,sha256=ugBksLGOHdtOLlEuRyyc59TrkYKu3rDf8JxEgiBSVao,6536
 spacr/gui_classify_app.py,sha256=Zi15ryc1ocYitRF4kyxlC27XxGyzfSPdvj2d6ZrSh7E,8446
@@ -26,29 +26,29 @@ spacr/gui_make_masks_app_v2.py,sha256=X3izTBXdCZDlkVe-fbG-jmCQtcAbmK0OIivjyWaLhu
 spacr/gui_mask_app.py,sha256=mhTl_XzXLFl8Tx3WYEMpdYB_qw9u5JJa0EdkvlcIzAE,10706
 spacr/gui_measure_app.py,sha256=_C1-XFL5HSquUEEbM_NcxdvHx-socPFCx85MBG4d6xo,10598
 spacr/gui_sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-spacr/gui_utils.py,sha256=n_juaV_-DspNab9NNncWauB9wKCd7lPcvoKsjKfWFrk,56436
+spacr/gui_utils.py,sha256=jnbvfovPGcwY_hmHudEryhSBG3hFOUsV_iNQSokGHpM,70160
 spacr/io.py,sha256=IoERqSwoxJrInYl-E0WfwFOEDZXFdJofk5DmpbyLGWM,112077
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
 spacr/make_masks_app.py,sha256=iGaTwhowoe2JMOSOf8bJwQZTooRhLQx7KO0ewnAmqDY,45138
 spacr/make_masks_app_v2.py,sha256=X3izTBXdCZDlkVe-fbG-jmCQtcAbmK0OIivjyWaLhug,30576
 spacr/mask_app.py,sha256=mhTl_XzXLFl8Tx3WYEMpdYB_qw9u5JJa0EdkvlcIzAE,10706
-spacr/measure.py,sha256=0FRsHF5ftar4JZ0B_6Nq-NlyP5t6aiO0IrskyikIBEE,55000
+spacr/measure.py,sha256=r5nxxULUyka2L5IVdnmEmnMywChY3a4DWGse3ygIh4Q,56000
 spacr/measure_app.py,sha256=_C1-XFL5HSquUEEbM_NcxdvHx-socPFCx85MBG4d6xo,10598
 spacr/old_code.py,sha256=jw67DAGoLBd7mWofVzRJSEmCI1Qrff26zIo65SEkV00,13817
 spacr/plot.py,sha256=lrwU51OTWfby1wx73XGyjYmTjLVia7WOmGH5LZZ-4jM,67145
 spacr/sequencing.py,sha256=U_TBJGNfOBfokGegUe950W_KPfm51VOgpfibXoZ8RMQ,83974
-spacr/settings.py,sha256=Tr2fo2I75FGfmEVQOONOpGwqXMzFCrYMz4NAxav3ckg,21183
+spacr/settings.py,sha256=ElHlNBNqvjtHFD7WC-QqKqXjMeosKXqJKnjeRX0mHVo,21456
 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=O7dpCF3bU95d2v0UuPFeJtzXYrkh0r-6aLxaqkKkFwY,184619
+spacr/utils.py,sha256=MM31yWquNDFmhxAU3l3Qx64peQJ6VWOuNGS6gkia5AY,186541
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model,sha256=z8BbHWZPRnE9D_BHO0fBREE85c1vkltDs-incs2ytXQ,26566572
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv,sha256=fBAGuL_B8ERVdVizO3BHozTDSbZUh1yFzsYK3wkQN68,420
 spacr/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.1.12.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.1.12.dist-info/METADATA,sha256=ppvYUfj-bd4G-fel8rkLsj8tR7J-7Fkh6sQupjufIqQ,5301
-spacr-0.1.12.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.1.12.dist-info/entry_points.txt,sha256=PxmdWbth1nQzQfE0s2M3XST_of47tBtlBPH20KJrvkE,354
-spacr-0.1.12.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.1.12.dist-info/RECORD,,
+spacr-0.1.50.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.1.50.dist-info/METADATA,sha256=5AUx1Qr2W-JmYcI3gGVkgO96mPAG01o8qj8_Mjlh6ho,5050
+spacr-0.1.50.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.1.50.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.1.50.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.1.50.dist-info/RECORD,,

spacr-0.1.50.dist-info/entry_points.txt

@@ -0,0 +1,8 @@
+[console_scripts]
+annotate = spacr.app_annotate:gui_annotate
+classify = spacr.app_classify:start_classify_app
+make_masks = spacr.app_make_masks:gui_make_masks
+mask = spacr.app_mask:start_mask_app
+measure = spacr.app_measure:start_measure_app
+sim = spacr.app_sim:gui_sim
+spacr = spacr.gui:gui_app

spacr-0.1.12.dist-info/entry_points.txt

@@ -1,9 +0,0 @@
-[console_scripts]
-annotate = spacr.annotate_app_v2:gui_annotate
-classify = spacr.gui_classify_app:gui_classify
-gui = spacr.gui:gui_app
-make_masks = spacr.gui_make_mask_app:gui_make_masks
-make_masks2 = spacr.gui_make_mask_app_v2:gui_make_masks
-mask = spacr.gui_mask_app:gui_mask
-measure = spacr.gui_measure_app:gui_measure
-sim = spacr.gui_sim_app:gui_sim