spacr 0.2.68__py3-none-any.whl → 0.3.0__py3-none-any.whl

spacr/settings.py

@@ -34,6 +34,7 @@ def set_default_settings_preprocess_generate_masks(src, settings={}):
     if 'src' not in settings:
         settings['src'] = 'path'
 
+    settings.setdefault('segmentation_mode', 'cellpose')
     settings.setdefault('preprocess', True)
     settings.setdefault('masks', True)
     settings.setdefault('save', True)
@@ -580,7 +581,7 @@ 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,
@@ -829,10 +830,11 @@ expected_types = {
     "custom_model_path":str,
     "generate_training_dataset":bool,
     'preload_batches':int,
+    "segmentation_mode":str,
     "train_DL_model":bool,
 }
 
-categories = {"General": ["src", "metadata_type", "custom_regex", "experiment", "channels", "magnification", "channel_dims", "apply_model_to_dataset", "generate_training_dataset", "train_DL_model"],
+categories = {"General": ["src", "metadata_type", "custom_regex", "experiment", "channels", "magnification", "channel_dims", "apply_model_to_dataset", "generate_training_dataset", "train_DL_model", "segmentation_mode"],
              "Cell": ["cell_intensity_range", "cell_size_range", "cell_chann_dim", "cell_channel", "cell_background", "cell_Signal_to_noise", "cell_CP_prob", "cell_FT", "remove_background_cell", "cell_min_size", "cell_mask_dim", "cytoplasm", "cytoplasm_min_size", "include_uninfected", "merge_edge_pathogen_cells", "adjust_cells"],
              "Nucleus": ["nucleus_intensity_range", "nucleus_size_range", "nucleus_chann_dim", "nucleus_channel", "nucleus_background", "nucleus_Signal_to_noise", "nucleus_CP_prob", "nucleus_FT", "remove_background_nucleus", "nucleus_min_size", "nucleus_mask_dim", "nucleus_loc"],
              "Pathogen": ["pathogen_intensity_range", "pathogen_size_range", "pathogen_chann_dim", "pathogen_channel", "pathogen_background", "pathogen_Signal_to_noise", "pathogen_CP_prob", "pathogen_FT", "pathogen_model", "remove_background_pathogen", "pathogen_min_size", "pathogen_mask_dim"],
@@ -883,6 +885,8 @@ 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 +1205,7 @@ 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 +1216,15 @@ 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()
@@ -1209,16 +1210,16 @@ def _calculate_recruitment(df, channel):
     for chan in channels:
         df[f'{object_type}_slope_channel_{chan}'] = 1
 
-    for chan in channels:
-        df[f'nucleus_coordinates_{chan}'] = df[[f'nucleus_channel_{chan}_centroid_weighted_local-0', f'nucleus_channel_{chan}_centroid_weighted_local-1']].values.tolist()
-        df[f'pathogen_coordinates_{chan}'] = df[[f'pathogen_channel_{chan}_centroid_weighted_local-0', f'pathogen_channel_{chan}_centroid_weighted_local-1']].values.tolist()
-        df[f'cell_coordinates_{chan}'] = df[[f'cell_channel_{chan}_centroid_weighted_local-0', f'cell_channel_{chan}_centroid_weighted_local-1']].values.tolist()
-        df[f'cytoplasm_coordinates_{chan}'] = df[[f'cytoplasm_channel_{chan}_centroid_weighted_local-0', f'cytoplasm_channel_{chan}_centroid_weighted_local-1']].values.tolist()
-
-        df[f'pathogen_cell_distance_channel_{chan}'] = df.apply(lambda row: np.sqrt((row[f'pathogen_coordinates_{chan}'][0] - row[f'cell_coordinates_{chan}'][0])**2 + 
-                                                      (row[f'pathogen_coordinates_{chan}'][1] - row[f'cell_coordinates_{chan}'][1])**2), axis=1)
-        df[f'nucleus_cell_distance_channel_{chan}'] = df.apply(lambda row: np.sqrt((row[f'nucleus_coordinates_{chan}'][0] - row[f'cell_coordinates_{chan}'][0])**2 + 
-                                                      (row[f'nucleus_coordinates_{chan}'][1] - row[f'cell_coordinates_{chan}'][1])**2), axis=1)
+    #for chan in channels:
+    #    df[f'nucleus_coordinates_{chan}'] = df[[f'nucleus_channel_{chan}_centroid_weighted_local-0', f'nucleus_channel_{chan}_centroid_weighted_local-1']].values.tolist()
+    #    df[f'pathogen_coordinates_{chan}'] = df[[f'pathogen_channel_{chan}_centroid_weighted_local-0', f'pathogen_channel_{chan}_centroid_weighted_local-1']].values.tolist()
+    #    df[f'cell_coordinates_{chan}'] = df[[f'cell_channel_{chan}_centroid_weighted_local-0', f'cell_channel_{chan}_centroid_weighted_local-1']].values.tolist()
+    #    df[f'cytoplasm_coordinates_{chan}'] = df[[f'cytoplasm_channel_{chan}_centroid_weighted_local-0', f'cytoplasm_channel_{chan}_centroid_weighted_local-1']].values.tolist()
+    # 
+    #    df[f'pathogen_cell_distance_channel_{chan}'] = df.apply(lambda row: np.sqrt((row[f'pathogen_coordinates_{chan}'][0] - row[f'cell_coordinates_{chan}'][0])**2 + 
+    #                                                  (row[f'pathogen_coordinates_{chan}'][1] - row[f'cell_coordinates_{chan}'][1])**2), axis=1)
+    #    df[f'nucleus_cell_distance_channel_{chan}'] = df.apply(lambda row: np.sqrt((row[f'nucleus_coordinates_{chan}'][0] - row[f'cell_coordinates_{chan}'][0])**2 + 
+    #                                                  (row[f'nucleus_coordinates_{chan}'][1] - row[f'cell_coordinates_{chan}'][1])**2), axis=1)
     return df
     
 def _group_by_well(df):
@@ -4443,3 +4444,5 @@ def get_cuda_version():
             return output.split('release ')[1].split(',')[0].replace('.', '')
     except (subprocess.CalledProcessError, FileNotFoundError):
         return None
+
+

{spacr-0.2.68.dist-info → spacr-0.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.68
+Version: 0.3.0
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -47,9 +47,17 @@ 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: importlib-metadata<4.0,>=3.6
 Requires-Dist: keyring<16.0,>=15.1
 Requires-Dist: screeninfo<1.0,>=0.8.1
+Requires-Dist: ipykernel
+Requires-Dist: gdown
+Requires-Dist: fastremap>=1.14.1
+Requires-Dist: monai>=1.3.0
+Requires-Dist: pytz>=2023.3.post1
+Requires-Dist: segmentation-models-pytorch>=0.3.3
+Requires-Dist: tifffile>=2023.4.12
+Requires-Dist: tqdm>=4.65.0
+Requires-Dist: wandb>=0.16.2
 Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest<3.11,>=3.9; extra == "dev"

{spacr-0.2.68.dist-info → spacr-0.3.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-spacr/__init__.py,sha256=8NZIlJOY2OzRCFjXvqusFL7BfyEJwNqB2lL8QNB-Kgo,1141
+spacr/__init__.py,sha256=bKVlCCJatRBMqjfxSXds2D_Swjf30T6agvAQ0Usz80o,1176
 spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
 spacr/app_annotate.py,sha256=nEIL7Fle9CDKGo3sucG_03DgjUQt5W1M1IHBIpVBr08,2171
 spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
@@ -8,24 +8,78 @@ 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=gOr5P58s4ubzDfO0Ar3Zwce0bo-E8qxdN37Ian82RGw,150744
 spacr/deep_spacr.py,sha256=a2YewgkQvLV-95NYJAutnojvJmX4S8z_wv6Tb-XIgUI,34484
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
-spacr/gui.py,sha256=RMg0bgbUpO6JwaWuNVMwuVZ18j4WlER3nW0Eaa0YZ30,7883
-spacr/gui_core.py,sha256=KAZmk1LHqI2WcB2-QO9De6mHAiDRQMU21nu5948UcF4,38745
-spacr/gui_elements.py,sha256=7YLyIeK5JFqzevzEruvfQOrfDGOS9ZgD8ZE-dxywp3g,122706
-spacr/gui_utils.py,sha256=pq_bmZ527S1j2s6McvqMhHNI05hJycBhHM8GY_jH9Ng,30597
-spacr/io.py,sha256=ZtVNbEom8X8p_KfsuWw0glGwLg6S0CfwwevDPGdfiSc,117342
+spacr/gui.py,sha256=zUkIyAuOwwoMDoExxtI-QHRfOhE1R2rulXJDNxwSLGc,7947
+spacr/gui_core.py,sha256=ZUIqvK7x6NzgrmuTRbvwCTTSpU3yWUaId6MZjXv16us,40128
+spacr/gui_elements.py,sha256=OA514FUVRKAcdu9CFVOt7UEzn1vztakQ-rDyKqV0b9A,129771
+spacr/gui_utils.py,sha256=DCI--DNoYDWY1q0Aohd0XwFqjdPM3K5kCgRKiJGTnfc,30697
+spacr/io.py,sha256=o2Sxan6_HylbYNUjNdgeQ4iEpcXRwlgV1r59J2HG0xQ,117292
 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/measure.py,sha256=ooMOP2OE0BHUNqIkg0ltwV2FiO6hZDIcRC6A0YmGcws,54875
+spacr/mediar.py,sha256=KEkrO0dlAbOr2tN4c8-vDncTy3IWNzUAwWYiPRofFqU,14864
+spacr/plot.py,sha256=9Ty2cMJpICXPCEE4inGTb1FvlUZkVgqB7lqJaggmjZE,73975
+spacr/sequencing.py,sha256=92KmjFa8Ptwmpf-GtyH3-uX6djFOYR5lJjMBHeciqhs,66921
+spacr/settings.py,sha256=PfIPLyMyBAfOodtdgNT8QzbysNDxTnsONXdI-fKtIDQ,68038
 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=D13hYJsVuq1ZMWYGyvtEskU_W2P8ddsI9zX9pTtMAFA,189159
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
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+spacr/resources/MEDIAR/LICENSE,sha256=yEj_TRDLUfDpHDNM0StALXIt6mLqSgaV2hcCwa6_TcY,1065
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+spacr/resources/MEDIAR/train_tools/data_utils/custom/NormalizeImage.py,sha256=7DfWVusYRRuEyA8eXujNyGJz0dubx7b7uhgEzzrh3-4,2152
+spacr/resources/MEDIAR/train_tools/data_utils/custom/__init__.py,sha256=SalCNvPyiy0rqLpjdoXPXGoWlKf-8K9vtDQ70HXOXe0,80
+spacr/resources/MEDIAR/train_tools/data_utils/custom/modalities.pkl,sha256=C1D7NkUZ5er7Kdeyhhwjo0IGUvCsVfKPBzcwfaORd8Q,3762
+spacr/resources/MEDIAR/train_tools/models/MEDIARFormer.py,sha256=UN8BYjraTNNdZUAGjl3yF566ERHAHQvj3GAQ6OETUOI,3615
+spacr/resources/MEDIAR/train_tools/models/__init__.py,sha256=CkY6rZxr-c9XxXNpQbYUYvHXDpf9E6rUmY1bQ47aEP8,28
+spacr/resources/MEDIAR_weights/.DS_Store,sha256=1lFlJ5EFymdzGAUAaI30vcaaLHt3F1LwpG7xILf9jsM,6148
 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
 "spacr/resources/font/open_sans/OpenSans-VariableFont_wdth,wght.ttf",sha256=E3RLvAefD0kuT7OxShXSQrjZYA-qzUI9WM35N_6nzms,529700
@@ -66,6 +120,7 @@ spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-MediumItalic.ttf,sh
 spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-Regular.ttf,sha256=skg4DCl15zL9ZD4MAL9fOt4WjonKYBUOMj46ItSAe5Q,130848
 spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-SemiBold.ttf,sha256=uCiR97jg6sUHtGKVPNtJEg1zZG5Y9ArQ-raqBGjaeGg,130856
 spacr/resources/font/open_sans/static/OpenSans_SemiCondensed-SemiBoldItalic.ttf,sha256=a5-0oOIrtJltQRa64uFKCdtcjzPvEJ71f_cYavG2i3E,137132
+spacr/resources/icons/.DS_Store,sha256=1lFlJ5EFymdzGAUAaI30vcaaLHt3F1LwpG7xILf9jsM,6148
 spacr/resources/icons/abort.png,sha256=avtIRT7aCJsdZ1WnY_rZStm6cCji5bYPLnlptdcTNcM,6583
 spacr/resources/icons/annotate.png,sha256=GFgh7DiUMwPG_-xE6W1qU8V_qzSwBi1xKenfoaQxeFA,15495
 spacr/resources/icons/cellpose_all.png,sha256=HVWOIOBF8p3-On-2UahwMyQXp7awsoC5yWExU1ahDag,20271
@@ -81,6 +136,7 @@ spacr/resources/icons/map_barcodes.png,sha256=ED6yCopk3hP7tICSvT8U_qA1bOOb0WHqmx
 spacr/resources/icons/mask.png,sha256=DcBes-3UJ7XjRfj_P4RttRp680ZKZeH9a-DSk7bIF5U,37658
 spacr/resources/icons/measure.png,sha256=Gd-dlN-3Z8D_XngJnChNme8D63KEJMFs_cBv7wT2vOY,40938
 spacr/resources/icons/ml_analyze.png,sha256=Wc9a_LpG2XffiMfXxn0yUmGP40IXzlAV7bHXQf7m_2o,15754
+spacr/resources/icons/plaque.png,sha256=NWt7C8thV0iQ1YuRvW_NfUJSFG6XK_iGpoW0R9Xfsyc,45033
 spacr/resources/icons/recruitment.png,sha256=dlVh2ebV_f3rhRFBiL0hDtlUeBSIeg0d4vny8A8IAdo,25067
 spacr/resources/icons/regression.png,sha256=WIrKY4fSojBOCDkHno4Qb-KH7jcHh6G67dOKzczaU1I,42267
 spacr/resources/icons/run.png,sha256=ICzyAvsRBCXNAbdn5N3PxCxxVyqxkfC4zOI5Zc8vbxQ,8974
@@ -89,12 +145,15 @@ spacr/resources/icons/settings.png,sha256=y5Ow5BxJDDsrqom0VNbOMDGGUs6odxbSMDy6y4
 spacr/resources/icons/spacr_logo_rotation.gif,sha256=bgIx1Hx41Ob90SY-q3PBa3CSxtVRnF9XX-ApUSr0wvY,1502560
 spacr/resources/icons/train_cellpose.png,sha256=_PZ_R_B6azuUACmscScAkugmgLZvCPKQFGIAsszqNLk,3858
 spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8bI,27457
+spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
+spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
+spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
 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
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