spacr 0.1.16__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-0.1.16.dist-info → spacr-0.1.50.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.16
+Version: 0.1.50
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -39,6 +39,7 @@ 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: huggingface-hub <0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest <3.11,>=3.9 ; extra == 'dev'
 Provides-Extra: full

{spacr-0.1.16.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=27NzovmbcSa-zdqo9WrFfBcggybhVQmKbgSBDTFnSvU,23588
-spacr/app_classify.py,sha256=7UKRGW245Chtxc_oCmyS-4omQpffvzzBvsHmC5ey4v8,8665
-spacr/app_make_masks.py,sha256=ksggY0xBWt7Fgbd451JOabA064kcjiDm8MTslUq1FLo,45088
-spacr/app_make_masks_v2.py,sha256=csZbUFhOfdHCQ1Wi21bgC1PG8ll5InMqUVmY3-90xlc,30543
-spacr/app_mask.py,sha256=dDZyIlI71vSMqBT3tC9I3BN8J0kxRf9-h5gBiI7pWZk,11357
-spacr/app_measure.py,sha256=jOhtqpO6BQSEpeUZA3taR9jThmo0J7BXMq1URzrdyjA,10841
+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=xyf2bmAck8OrbYlvNLpY6rs4EuhuCOxff3f8ZcEZHBQ,6594
+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=emUGYxxk9LOsYk2ozLc6mfglzeb4WqBwYhXwitLLJBA,58746
+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-0.1.16.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.1.16.dist-info/METADATA,sha256=-VoJLJbzVVNvGhVmWA2uh5DydW0W4KjiCnz5WYwgLlQ,5004
-spacr-0.1.16.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.1.16.dist-info/entry_points.txt,sha256=e6tBSk-bac5ypML_iWIROnQ-hDSLZT_sGpGviPNHG4g,277
-spacr-0.1.16.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.1.16.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-0.1.16.dist-info/entry_points.txt

@@ -1,8 +0,0 @@
-[console_scripts]
-annotate = spacr.app_annotate:gui_annotate
-classify = spacr.app_classify:gui_classify
-make_masks = spacr.app_make_mask:gui_make_masks
-mask = spacr.app_mask:gui_mask
-measure = spacr.app_measure:gui_measure
-sim = spacr.app_sim:gui_sim
-spacr = spacr.gui:gui_app