spacr 0.2.21__py3-none-any.whl → 0.2.31__py3-none-any.whl

spacr/utils.py

@@ -87,6 +87,61 @@ 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):
+        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 not isinstance(files_processed, int):
+        try:
+            files_processed = int(files_processed)
+        except:
+            files_processed = 0
+    if not isinstance(files_to_process, int):
+        try:
+            files_to_process = int(files_to_process)
+        except:
+            files_to_process = 0
+
+    time_info = ""
+    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:
+            time_info = f'Time/image: {average_time:.3f}sec, Time_left: {time_left:.3f} min.'
+        else:
+            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.'
+
+    print(f'Progress: {files_processed}/{files_to_process}, operation_type: {operation_type} {time_info}')
+
+
+
 def reset_mp():
     current_method = get_start_method()
     system = platform.system()

{spacr-0.2.21.dist-info → spacr-0.2.31.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.21
+Version: 0.2.31
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.2.21.dist-info → spacr-0.2.31.dist-info}/RECORD

@@ -1,6 +1,6 @@
 spacr/__init__.py,sha256=pJ7Mm7Kb1DhHIdLmNgMILFVWJ9QAG47pT0M6wtiXl8E,1465
 spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
-spacr/app_annotate.py,sha256=xA39bsgvrQlY8P22cUC7sAaw4O57tgZawZtsANmY0ek,2302
+spacr/app_annotate.py,sha256=nEIL7Fle9CDKGo3sucG_03DgjUQt5W1M1IHBIpVBr08,2171
 spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
 spacr/app_make_masks.py,sha256=pqDhRpluiHZz-kPX2Zh_KbYe4TsU43qYBa_7f-rsjpw,1694
 spacr/app_mask.py,sha256=l-dBY8ftzCMdDe6-pXc2Nh_u-idNL9G7UOARiLJBtds,153
@@ -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=wL6E1MMNrRyvyileqsTOnQ3lhABnw_L6O-4UApZGL84,160216
+spacr/core.py,sha256=iAH6de2dW0nKVtVeBjdWOhSW_KoHlVDVOoOsHb6vGC0,148884
 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=ay1IMMjcJLk8GeaXdL5rzu8xkJmpy_5XzqNhET_4SaI,33199
-spacr/gui_elements.py,sha256=X3-uReDPCuvYSjNi9UyUALle7K-DKjaiEA5uHvczwa4,79701
-spacr/gui_utils.py,sha256=CuGB7rN_VCGu5FP9ZeBTrIYBzqQlylX-uszVyYcF0VM,13899
-spacr/io.py,sha256=f7cVn48wNUEj6Teky4p3ojoivAdMUmPll2s0MzJkKD0,112068
+spacr/gui_core.py,sha256=4II8TscaDHDvRXc4D-azQyAeVGNkqyN6_HaNhkjij4s,35546
+spacr/gui_elements.py,sha256=XGM88u7acPO6ulRE4QJwD72-POcN-pKJhseRkJLELzo,96179
+spacr/gui_utils.py,sha256=ySSDDYmY80h_Wk2Nb1oxbugRU2TWt6N7BwusUl_-wRo,14970
+spacr/io.py,sha256=Dehuqn_oGo0gcyezQIw9rUUvO7oOHDWuMkPDSCgyrp8,115521
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
-spacr/measure.py,sha256=RzcD8rsUaOZUYB-zcbaUZcJbrwT0IIW5G7qvb__SO-E,55616
+spacr/measure.py,sha256=W5_yuLnsFSafuZNcKzVsCTJSTfpbNgrGTuxG1OVb0iU,55283
 spacr/plot.py,sha256=DYJEoK1kz2ih6ZGvKiA3xTqeIeKQNhuQKwgrscopFxA,69101
 spacr/sequencing.py,sha256=fHZRnoMSxmhMdadkei3lUeBdckqFyptWdQyWsDW3aaU,83304
-spacr/settings.py,sha256=2fAyGl8lzkkpB3MJJoywo0hCEg9CjziLWkXF0Miv3mM,65569
+spacr/settings.py,sha256=deX0pNwTqyHojpCTiF060RSK5oPeSEcS_s6UlVc0x3Q,65442
 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=OQ8sSBH6VWx2xP_vh4ILJT71B46DFFhsq-Y6WxYdGhI,186891
+spacr/utils.py,sha256=r23Cd94HT3q1kMIbyEmyvJVnnDOY16plvUXVwxuX1PE,189256
 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
@@ -37,20 +37,22 @@ spacr/resources/icons/logo_spacr.png,sha256=g9y2ZmnV3hab8r1idDfytm8AaHbBiQdu_93J
 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
-spacr/resources/icons/measure.png,sha256=IxjBHJQ_UWPRY3aaLNEvgpb_v9LCF_2kovz2Ms0LrFM,49442
-spacr/resources/icons/recruitment.png,sha256=vuXOU7sSQ306zLx63BsXnoftAsdyJ3ORsi5uk9qAO2M,39730
+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/recruitment.png,sha256=dlVh2ebV_f3rhRFBiL0hDtlUeBSIeg0d4vny8A8IAdo,25067
 spacr/resources/icons/regression.png,sha256=WIrKY4fSojBOCDkHno4Qb-KH7jcHh6G67dOKzczaU1I,42267
 spacr/resources/icons/run.png,sha256=ICzyAvsRBCXNAbdn5N3PxCxxVyqxkfC4zOI5Zc8vbxQ,8974
 spacr/resources/icons/sequencing.png,sha256=P9E_Y76ZysWMKst3_hAw-_4F510XPW1l1TsDElVzt4o,17775
 spacr/resources/icons/settings.png,sha256=y5Ow5BxJDDsrqom0VNbOMDGGUs6odxbSMDy6y4r_F0w,22269
-spacr/resources/icons/train_cellpose.png,sha256=GAkaWVLkOzaUvJXKIT-hMcI7EFr4Qd18MIPt8YZIIsU,5811
+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/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-0.2.21.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.2.21.dist-info/METADATA,sha256=AFomPaRGBZpEzyyW8AEWyuBUyBkHs6PwSJzC2GFjOcU,5050
-spacr-0.2.21.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.2.21.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.2.21.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.2.21.dist-info/RECORD,,
+spacr-0.2.31.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.2.31.dist-info/METADATA,sha256=avO1ZcgZs-TVLFdCBmxznpwuIH0Cehk29AuUOmFeVKM,5050
+spacr-0.2.31.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.2.31.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.2.31.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.2.31.dist-info/RECORD,,