spacr 0.2.67__py3-none-any.whl → 0.2.81__py3-none-any.whl

spacr/settings.py

@@ -580,7 +580,7 @@ expected_types = {
     "timelapse": bool,
     "timelapse_displacement": int,
     "timelapse_memory": int,
-    "timelapse_frame_limits": list,  # This can be a list of lists
+    "timelapse_frame_limits": (list, type(None)),  # This can be a list of lists
     "timelapse_remove_transient": bool,
     "timelapse_mode": str,
     "timelapse_objects": list,
@@ -883,6 +883,8 @@ def check_settings(vars_dict, expected_types, q=None):
                         settings[key] = parsed_value
                     else:
                         raise ValueError("Invalid format: Mixed list and list of lists")
+                #elif parsed_value == None:
+                #    settings[key] = None
                 else:
                     raise ValueError("Invalid format for list or list of lists")
             elif expected_type == list:
@@ -1201,7 +1203,7 @@ descriptions = {
 def set_annotate_default_settings(settings):
     settings.setdefault('src', 'path')
     settings.setdefault('image_type', 'cell_png')
-    settings.setdefault('channels', "'r','g','b'")
+    settings.setdefault('channels', "r,g,b")
     settings.setdefault('img_size', 200)
     settings.setdefault('annotation_column', 'test')
     settings.setdefault('normalize', 'False')
@@ -1212,13 +1214,15 @@ def set_annotate_default_settings(settings):
 
 def set_default_generate_barecode_mapping(settings={}):
     settings.setdefault('src', 'path')
+    settings.setdefault('target_sequence', 'TGCTGTTTCCAGCATAGCTCTTAAAC')
+    settings.setdefault('offset_start', -8)
+    settings.setdefault('expected_end', 89)
+    settings.setdefault('column_csv', '/home/carruthers/Documents/column_barcodes.csv')
+    settings.setdefault('grna_csv', '/home/carruthers/Documents/grna_barcodes.csv')
+    settings.setdefault('row_csv', '/home/carruthers/Documents/row_barcodes.csv')
+    settings.setdefault('save_h5', True)
+    settings.setdefault('comp_type', 'zlib')
+    settings.setdefault('comp_level', 5)
     settings.setdefault('chunk_size', 100000)
-    
-    settings.setdefault('barcode_mapping', {'row': ['/home/carruthers/Documents/row_barcodes.csv',(80, 88), True],
-                                            'grna': ['/home/carruthers/Documents/grna_barcodes.csv',(34, 55), True],
-                                            'column': ['/home/carruthers/Documents/column_barcodes.csv',(0, 7), False]})
-    
     settings.setdefault('n_jobs', None)
-    settings.setdefault('compression', 'zlib')
-    settings.setdefault('complevel', 5)
     return settings

spacr/utils.py

@@ -123,7 +123,8 @@ def print_progress(files_processed, files_to_process, n_jobs, time_ls=None, batc
             average_time_img = average_time / batch_size
             time_info = f'Time/batch: {average_time:.3f}sec, Time/image: {average_time_img:.3f}sec, Time_left: {time_left:.3f} min.'
     else:
-        print(f'Progress: {files_processed}/{files_to_process}, operation_type: {operation_type} {time_info}')
+        time_info = None
+    print(f'Progress: {files_processed}/{files_to_process}, operation_type: {operation_type}, {time_info}')
 
 def reset_mp():
     current_method = get_start_method()
@@ -4443,3 +4444,5 @@ def get_cuda_version():
             return output.split('release ')[1].split(',')[0].replace('.', '')
     except (subprocess.CalledProcessError, FileNotFoundError):
         return None
+
+

{spacr-0.2.67.dist-info → spacr-0.2.81.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.67
+Version: 0.2.81
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -47,6 +47,9 @@ Requires-Dist: gpustat<2.0,>=1.1.1
 Requires-Dist: pyautogui<1.0,>=0.9.54
 Requires-Dist: tables<4.0,>=3.8.0
 Requires-Dist: rapidfuzz<4.0,>=3.9
+Requires-Dist: keyring<16.0,>=15.1
+Requires-Dist: screeninfo<1.0,>=0.8.1
+Requires-Dist: ipykernel
 Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest<3.11,>=3.9; extra == "dev"

{spacr-0.2.67.dist-info → spacr-0.2.81.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=IDme9j7eeC_49KGaNk_xPOKtpxdcXKMhYtoo3xhjQMM,146502
+spacr/core.py,sha256=B2KMyG6IrVtV9d4XQkXVblbvfFhgcMY2o-mtmqDVDic,146519
 spacr/deep_spacr.py,sha256=a2YewgkQvLV-95NYJAutnojvJmX4S8z_wv6Tb-XIgUI,34484
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
-spacr/gui.py,sha256=q8SBFiMeU6Sy3orpzHdsFxvURr5zv-S-9DOD3TEQ6ag,7445
-spacr/gui_core.py,sha256=KAZmk1LHqI2WcB2-QO9De6mHAiDRQMU21nu5948UcF4,38745
-spacr/gui_elements.py,sha256=7YLyIeK5JFqzevzEruvfQOrfDGOS9ZgD8ZE-dxywp3g,122706
-spacr/gui_utils.py,sha256=1pZ9QAh6BCVb6BSXciU0V9qFWOSsTtCiC72iGXUdV0c,29941
+spacr/gui.py,sha256=RMg0bgbUpO6JwaWuNVMwuVZ18j4WlER3nW0Eaa0YZ30,7883
+spacr/gui_core.py,sha256=gTgsBzhZ5Q4vl6fT8VwrHWZ6BXWW5FNli8CE3WNMfv0,39986
+spacr/gui_elements.py,sha256=OA514FUVRKAcdu9CFVOt7UEzn1vztakQ-rDyKqV0b9A,129771
+spacr/gui_utils.py,sha256=pq_bmZ527S1j2s6McvqMhHNI05hJycBhHM8GY_jH9Ng,30597
 spacr/io.py,sha256=ZtVNbEom8X8p_KfsuWw0glGwLg6S0CfwwevDPGdfiSc,117342
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
 spacr/measure.py,sha256=4rmzH_a5Y0s1qALVi6YRut3xpnkJXs5vzeTPCEf3QS8,54871
 spacr/plot.py,sha256=xVnbML7WpAEzdJdrLeYRk6aPinZSiV2dLAeu4mh7n0k,73963
-spacr/sequencing.py,sha256=y7EB8226B0b0gnGXt6jqBaFVATrM1Y89v3rtHb8XR_k,75746
-spacr/settings.py,sha256=tDvTBWANeuI6YC_fH5vK2HOOuRgQXIkzyNKDmt1vL4c,67745
+spacr/sequencing.py,sha256=92KmjFa8Ptwmpf-GtyH3-uX6djFOYR5lJjMBHeciqhs,66921
+spacr/settings.py,sha256=rxXvpbNSFL5GKluGCLu4sEsYg8oo8djtbnGXPJ5d8hc,67931
 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=R8PA8MyldBKQOvITo9f4oVFcKOMKv5gaD9T86T_LrEA,189120
+spacr/utils.py,sha256=OY65COsdaCFK04irC0L7tNPaOvI2x7PBIs9D9t-ToCg,189144
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/font/open_sans/OFL.txt,sha256=bGMoWBRrE2RcdzDiuYiB8A9OVFlJ0sA2imWwce2DAdo,4484
 "spacr/resources/font/open_sans/OpenSans-Italic-VariableFont_wdth,wght.ttf",sha256=QSoWv9h46CRX_fdlqFM3O2d3-PF3R1srnb4zUezcLm0,580280
@@ -92,9 +92,9 @@ 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-0.2.67.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.2.67.dist-info/METADATA,sha256=hBFthB5eIFRbvShTOF1ELiRLUdrfbSEEFvZTcgLSz00,5291
-spacr-0.2.67.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-spacr-0.2.67.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.2.67.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.2.67.dist-info/RECORD,,
+spacr-0.2.81.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.2.81.dist-info/METADATA,sha256=-3NGByY_rn0wM09SI0-XgrLr9UBdK09AlU3TtaaGJOg,5389
+spacr-0.2.81.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+spacr-0.2.81.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.2.81.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.2.81.dist-info/RECORD,,