spacr 0.9.3__py3-none-any.whl → 0.9.4__py3-none-any.whl

spacr/io.py

@@ -1587,7 +1587,7 @@ def preprocess_img_data(settings):
         print(f"Found {extension_counts[most_common_extension]} {most_common_extension} files")
     
     else:
-        print(f"Could not find any {valid_ext} files in {src} only found {extension_counts[0]}")
+        print(f"Could not find any {valid_ext} files in {src}")
         print(f"{files} in {src}")
         print(f"Please check the folder and try again")
         

spacr/settings.py

@@ -1053,7 +1053,7 @@ def check_settings(vars_dict, expected_types, q=None):
         expected_type = expected_types.get(key, str)
 
         try:
-            if key in ["cell_plate_metadata", "timelapse_frame_limits", "png_size", "png_dims", "pathogen_plate_metadata", "treatment_plate_metadata", "timelapse_objects", "class_metadata", "crop_mode"]:
+            if key in ["cell_plate_metadata", "timelapse_frame_limits", "png_size", "png_dims", "pathogen_plate_metadata", "treatment_plate_metadata", "timelapse_objects", "class_metadata", "crop_mode", "dialate_png_ratios"]:
                 if value is None:
                     parsed_value = None
                 else:

spacr/sp_stats.py

@@ -7,7 +7,6 @@ from scipy.stats import chi2_contingency, fisher_exact
 import itertools
 from statsmodels.stats.multitest import multipletests
 
-
 def choose_p_adjust_method(num_groups, num_data_points):
     """
     Selects the most appropriate p-value adjustment method based on data characteristics.

{spacr-0.9.3.dist-info → spacr-0.9.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.9.3
+Version: 0.9.4
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -13,7 +13,7 @@ License-File: LICENSE
 Requires-Dist: numpy <2.0,>=1.26.4
 Requires-Dist: pandas <3.0,>=2.2.1
 Requires-Dist: scipy <2.0,>=1.12.0
-Requires-Dist: cellpose <4.0,>=3.0.6
+Requires-Dist: cellpose <5.0,>=4.0
 Requires-Dist: scikit-image <1.0,>=0.22.0
 Requires-Dist: scikit-learn <2.0,>=1.4.1
 Requires-Dist: scikit-posthocs <0.20,>=0.10.0
@@ -195,6 +195,13 @@ The following example Jupyter notebooks illustrate common workflows using spaCR.
 - `Finetune cellpose models <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/5_spacr_train_cellpose.ipynb>`_  
   *Finetune Cellpose models using your own annotated training data for improved segmentation accuracy.*
 
+Interactive Tutorial (under construction)
+-----------------------------------------
+
+Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
+
+`spaCR Tutorial Page <https://einarolafsson.github.io/spacr/tutorial/>`_
+
 License
 -------
 spaCR is distributed under the terms of the MIT License.

{spacr-0.9.3.dist-info → spacr-0.9.4.dist-info}/RECORD

@@ -14,7 +14,7 @@ spacr/gui.py,sha256=NhMh96KoArrSAaJBV6PhDQpIC1cQpxgb6SclhRbYG8s,8122
 spacr/gui_core.py,sha256=RtpdB8S8yF9WARRsUjrZ1szZi4ZMfG7R_W34BTBEGYo,52729
 spacr/gui_elements.py,sha256=OTU7aeLrPiMUTnyCT-J7ygng3beI9tdA0MmypOavEkw,156123
 spacr/gui_utils.py,sha256=F6KfNY3OqNkvfkOP1rxwBha5IOdLVyBgqZYPw3xPLes,42293
-spacr/io.py,sha256=SYLhupKnOJJscNSGE4N67E32-ywhwrjRccIfZrL38Uk,157966
+spacr/io.py,sha256=P6k3BYsy8VM0p7ficy2Ae4xTPb6tZM4xq47pY57-GBk,157933
 spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
 spacr/measure.py,sha256=nYvrfVfCIqD1AUk4QBE2jtpeSFtLdfUcnkhkqf9G4xQ,60877
 spacr/mediar.py,sha256=p0F515eFbm6_rePSnChsgqrgH-H5Sr_3zWrghtOnAUg,14863
@@ -22,9 +22,9 @@ spacr/ml.py,sha256=XCRZeX7UkbMctQICIoskeWVx8CCmmCoHNauUOAkfFq0,91692
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
 spacr/plot.py,sha256=Y1ON8Bu-FsZZZasXIK7nvnOohFzucCvFhyPE2bDGz1A,167340
 spacr/sequencing.py,sha256=EY12RdW5QRKpHDRQCw1QoAlxCq8FK2v6WoVa5uuDBXQ,26745
-spacr/settings.py,sha256=gT0FEP6anfhM6sbFofmLRhOwaQptgpcI18VX6nRqmtQ,87661
+spacr/settings.py,sha256=YpGfMzNgHGpqamfZ0wVoVG64UOb0rW9lfxCc9W4g7Ss,87683
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
-spacr/sp_stats.py,sha256=mbhwsyIqt5upsSD346qGjdCw7CFBa0tIS7zHU9e0jNI,9536
+spacr/sp_stats.py,sha256=C93Xe5fphQOKthw4Tmj8pHx-Nb1houIL-YYVIfmnQPg,9535
 spacr/spacr_cellpose.py,sha256=RBHMs2vwXcfkj0xqAULpALyzJYXddSRycgZSzmwI7v0,14755
 spacr/submodules.py,sha256=Z2i4kv_rWdxqoXsOKCF7BaSXtvaCZB69Ow8_FQBnZsY,83093
 spacr/timelapse.py,sha256=-5ZupTsCCpbenIQ2zsUmnwXh45B82fO-gPrSXOxu2s8,42980
@@ -103,9 +103,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 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-0.9.3.dist-info/LICENSE,sha256=t0Pov6pnK8thLteoF4xZGmdCwe5mhNwl3OXxLYTGD9U,1081
-spacr-0.9.3.dist-info/METADATA,sha256=67z09Wghste6IUXWFchysvsqH38M6GVnr9IgHYixVNg,10088
-spacr-0.9.3.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
-spacr-0.9.3.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.9.3.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.9.3.dist-info/RECORD,,
+spacr-0.9.4.dist-info/LICENSE,sha256=t0Pov6pnK8thLteoF4xZGmdCwe5mhNwl3OXxLYTGD9U,1081
+spacr-0.9.4.dist-info/METADATA,sha256=rEwXv8HSYOVMSYZpzjNXFds9XEIlk0y85AsxsZbGbGc,10324
+spacr-0.9.4.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
+spacr-0.9.4.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.9.4.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.9.4.dist-info/RECORD,,