spacr 0.3.45__py3-none-any.whl → 0.3.46__py3-none-any.whl

spacr/__init__.py

@@ -63,10 +63,10 @@ __all__ = [
 logging.basicConfig(filename='spacr.log', level=logging.INFO,
                     format='%(asctime)s:%(levelname)s:%(message)s')
 
-from spacr.utils import download_models
+from .utils import download_models
 
 # Check if models already exist
-models_dir = os.path.join(os.path.dirname(__file__), 'resources', 'models', 'cp')
-if not os.path.exists(models_dir) or not os.listdir(models_dir):
-    print("Models not found, downloading...")
-    download_models(local_dir=models_dir)
+#models_dir = os.path.join(os.path.dirname(__file__), 'resources', 'models', 'cp')
+#if not os.path.exists(models_dir) or not os.listdir(models_dir):
+#    print("Models not found, downloading...")
+download_models()

spacr/plot.py

@@ -3103,6 +3103,7 @@ def plot_data_from_csv(settings):
         save=settings['save'],                       # Whether to save the plot and results
         y_lim=settings['y_lim'],                     # Starting point for y-axis (optional)
         log_y=settings['log_y'],                     # Log-transform the y-axis
+        log_x=settings['log_x'],                     # Log-transform the x-axis
         error_bar_type='std',                        # Type of error bar ('std' or 'sem')
         representation=settings['representation'],
         theme=settings['theme'],                     # Seaborn color palette theme (e.g., 'pastel', 'muted')
@@ -3148,16 +3149,16 @@ def plot_region(settings):
     fig_3 = plot_image_grid(image_paths=activation_paths, percentiles=settings['percentiles'])
     fig_2 = plot_image_grid(image_paths=png_paths, percentiles=settings['percentiles'])
     fig_1 = plot_image_mask_overlay(file=fov_path,
-                                  channels=settings['channels'],
-                                  cell_channel=settings['cell_channel'],
-                                  nucleus_channel=settings['nucleus_channel'],
-                                  pathogen_channel=settings['pathogen_channel'],
-                                  figuresize=10,
-                                  percentiles=settings['percentiles'],
-                                  thickness=3, 
-                                  save_pdf=False, 
-                                  mode=settings['mode'],
-                                  export_tiffs=settings['export_tiffs'])
+                                    channels=settings['channels'],
+                                    cell_channel=settings['cell_channel'],
+                                    nucleus_channel=settings['nucleus_channel'],
+                                    pathogen_channel=settings['pathogen_channel'],
+                                    figuresize=10,
+                                    percentiles=settings['percentiles'],
+                                    thickness=3, 
+                                    save_pdf=False, 
+                                    mode=settings['mode'],
+                                    export_tiffs=settings['export_tiffs'])
     
     dst = os.path.join(settings['src'], 'results', name)
     save_figure_as_pdf(fig_1, os.path.join(dst, f"{name}_mask_overlay.pdf"))

{spacr-0.3.45.dist-info → spacr-0.3.46.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.45
+Version: 0.3.46
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.3.45.dist-info → spacr-0.3.46.dist-info}/RECORD

@@ -1,4 +1,4 @@
-spacr/__init__.py,sha256=3TNo4PgxHZTHOhyPc8AORvG3tzdPFEc30KAtsOou174,1618
+spacr/__init__.py,sha256=CZtAdU5etLcb9dVmz-4Y7Hjhw3ubjMzfjG0L5ybyFVA,1592
 spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
 spacr/app_annotate.py,sha256=zGmAJplDOckhaUZijkHgbFH9LJNbd6TolU2hamplOBc,2769
 spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
@@ -20,7 +20,7 @@ spacr/measure.py,sha256=KdboGXoi85BO5-_6er7932FgjFI7G7tuaQDnWSiEuew,54817
 spacr/mediar.py,sha256=FwLvbLQW5LQzPgvJZG8Lw7GniA2vbZx6Jv6vIKu7I5c,14743
 spacr/ml.py,sha256=bPcKVk1camnOhv8jQglj6EYyipAxxmiB1QJ2Fdo3dEM,50654
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
-spacr/plot.py,sha256=c7PYi4p-ARjHjHCoSn-8ZEXAit0WcTRVxAcAs47tLms,145287
+spacr/plot.py,sha256=r4kbrMA8iQ317f0lvIDj4wJDIDwDXXYHEgGtFJrO3-k,145387
 spacr/sequencing.py,sha256=t18mgpK6rhWuB1LtFOsPxqgpFXxuUmrD06ecsaVQ0Gw,19655
 spacr/settings.py,sha256=3ygnAY6uLtkzFQdK8TMBbWV6zXEX-G_wV19YLyjCBeM,77668
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
@@ -150,9 +150,9 @@ 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-0.3.45.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.3.45.dist-info/METADATA,sha256=eUCjysKj_sil9xg7E1ZQzIUGN8mCTYd1uw64MEY7cbo,5949
-spacr-0.3.45.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-spacr-0.3.45.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.3.45.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.3.45.dist-info/RECORD,,
+spacr-0.3.46.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.3.46.dist-info/METADATA,sha256=rDVd_7S8qknwKjW3gzWpaC4FvKLLArfmA3xqGlby088,5949
+spacr-0.3.46.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+spacr-0.3.46.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.3.46.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.3.46.dist-info/RECORD,,