spacr 0.1.6__py3-none-any.whl → 0.1.8__py3-none-any.whl

spacr/utils.py

@@ -74,9 +74,18 @@ from scipy import stats
 from .logger import log_function_call
 from multiprocessing import set_start_method, get_start_method
 
-import tkinter as tk
-from tkinter import ttk
-import tkinter.font as tkFont
+import torch
+import torchvision.transforms as transforms
+from torchvision.models import resnet50
+from PIL import Image
+import numpy as np
+import umap
+import pandas as pd
+from sklearn.ensemble import RandomForestClassifier
+from sklearn.preprocessing import StandardScaler
+from scipy.stats import f_oneway, kruskal
+from sklearn.cluster import KMeans
+from scipy import stats
 
 def reset_mp():
     current_method = get_start_method()
@@ -472,7 +481,7 @@ def is_list_of_lists(var):
         return True
     return False
 
-def normalize_to_dtype(array, p1=2, p2=98, percentile_list=None):
+def normalize_to_dtype(array, p1=2, p2=98, percentile_list=None, new_dtype=None):
     """
     Normalize each image in the stack to its own percentiles.
 
@@ -491,7 +500,16 @@ def normalize_to_dtype(array, p1=2, p2=98, percentile_list=None):
     The normalized stack with the same shape as the input stack.
     """
 
-    out_range = (0, np.iinfo(array.dtype).max)
+    if new_dtype is None:
+        out_range = (0, np.iinfo(array.dtype).max)
+    elif new_dtype in [np.uint8, np.uint16]:
+        out_range = (0, np.iinfo(new_dtype).max)
+    elif new_dtype in ['uint8', 'uint16']:
+        new_dtype = np.uint8 if new_dtype == 'uint8' else np.uint16
+        out_range = (0, np.iinfo(new_dtype).max)
+    else:
+        out_range = (0, np.iinfo(array.dtype).max)
+
     nimg = array.shape[2]
     new_stack = np.empty_like(array, dtype=array.dtype)
 
@@ -3844,18 +3862,6 @@ def search_reduction_and_clustering(numeric_data, n_neighbors, min_dist, metric,
     if verbose:
         print(f'Embedding shape: {embedding.shape}')
     return embedding, labels
-import torch
-import torchvision.transforms as transforms
-from torchvision.models import resnet50
-from PIL import Image
-import numpy as np
-import umap
-import pandas as pd
-from sklearn.ensemble import RandomForestClassifier
-from sklearn.preprocessing import StandardScaler
-from scipy.stats import f_oneway, kruskal
-from sklearn.cluster import KMeans
-from scipy import stats
 
 def load_image(image_path):
     """Load and preprocess an image."""
@@ -4050,7 +4056,7 @@ def _merge_cells_based_on_parasite_overlap(parasite_mask, cell_mask, nuclei_mask
     
     # Relabel the merged cell mask
     relabeled_cell_mask, _ = label(cell_mask, return_num=True)
-    return relabeled_cell_mask
+    return relabeled_cell_mask.astype(np.uint16)
 
 def adjust_cell_masks(parasite_folder, cell_folder, nuclei_folder, overlap_threshold=5, perimeter_threshold=30):
 
@@ -4090,7 +4096,7 @@ def adjust_cell_masks(parasite_folder, cell_folder, nuclei_folder, overlap_thres
         merged_cell_mask = _merge_cells_based_on_parasite_overlap(parasite_mask, cell_mask, nuclei_mask, overlap_threshold, perimeter_threshold)
         
         # Force 16 bit
-        mamerged_cell_masksk = merged_cell_mask.astype(np.uint16)
+        #merged_cell_mask = merged_cell_mask.astype(np.uint16)
         
         # Overwrite the original cell mask file with the merged result
         np.save(cell_path, merged_cell_mask)

{spacr-0.1.6.dist-info → spacr-0.1.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.6
+Version: 0.1.8
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.1.6.dist-info → spacr-0.1.8.dist-info}/RECORD

@@ -1,11 +1,11 @@
-spacr/__init__.py,sha256=264p0eJQFhj0zOrpcdxd4JUvofl9-dlzy-DwOyyO_kI,1442
+spacr/__init__.py,sha256=8uhfJ_RcnX4OmvflNRcts4zxnyfML6xiyIeFGZeMpXg,1416
 spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
 spacr/alpha.py,sha256=Y95sLEfpK2OSYKRn3M8eUOU33JJeXfV8zhrC4KnwSTY,35244
 spacr/annotate_app.py,sha256=imQ7ZEXDyM6ce1dxZ1xUS1-KequuF_NCI4xCaPLjvco,29275
 spacr/annotate_app_v2.py,sha256=imQ7ZEXDyM6ce1dxZ1xUS1-KequuF_NCI4xCaPLjvco,29275
-spacr/app_annotate.py,sha256=QKWQ0GGiKu5ik14OB4Z3YIqIJYpmsNJlqpnfnQPowAM,23563
+spacr/app_annotate.py,sha256=FhyDBsLdo6etOSvz6et2AhhJn67SwdeYUVDzBJzdw1E,2274
 spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
-spacr/app_make_masks.py,sha256=0N8Wfby3HaVX4m9tOyBy7OQolamYG9lVwmnlzkK4uaE,44993
+spacr/app_make_masks.py,sha256=qV3L_2TilGZBAUyBrzaWAayei_tf3XvJdUUDyzEI6hA,1834
 spacr/app_make_masks_v2.py,sha256=OkNeskNbgep8wQa4ES3jpJjZLfn4yIkGwQOd9r0spfA,30497
 spacr/app_mask.py,sha256=l-dBY8ftzCMdDe6-pXc2Nh_u-idNL9G7UOARiLJBtds,153
 spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
@@ -14,47 +14,47 @@ spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
 spacr/classify_app.py,sha256=Zi15ryc1ocYitRF4kyxlC27XxGyzfSPdvj2d6ZrSh7E,8446
 spacr/cli.py,sha256=507jfOOEV8BoL4eeUcblvH-iiDHdBrEVJLu1ghAAPSc,1800
-spacr/core.py,sha256=S44olGF8qveg6uBCRDuCP4FZ5dXXVwSfeImolTpQIAs,160372
-spacr/deep_spacr.py,sha256=rvqOoY9dadcTcKiABf61Nb8HEMVp1NouFmtAE2ee1T4,37056
+spacr/core.py,sha256=bm1cApGVTE218Ds3FqqWD5TsF5FF8kclHwPlvdOolzc,160216
+spacr/deep_spacr.py,sha256=ASBsN4JpHp_3S-91JUsB34IWTjTGPYI7jKV2qZnUR5M,37005
 spacr/foldseek.py,sha256=YIP1d4Ci6CeA9jSyiv-HTDbNmAmcSM9Y_DaOs7wYzLY,33546
 spacr/get_alfafold_structures.py,sha256=ehx_MQgb12k3hFecP6cYVlm5TLO8iWjgevy8ESyS3cw,3544
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
-spacr/gui.py,sha256=kvQ0X9nyZz_BWsOyJSNSv7gEG1ZuTqjz4EH78e0uul4,7783
+spacr/gui.py,sha256=OPIMDVVYyAKO3zJIrWkP_YIc9-SwQsVR2S7ynXu1wkQ,8901
 spacr/gui_2.py,sha256=ZAI5quQYbhQJ40vK0NCqU_UMSPLkpfeQpomBWUSM0fc,6946
 spacr/gui_annotate.py,sha256=ugBksLGOHdtOLlEuRyyc59TrkYKu3rDf8JxEgiBSVao,6536
 spacr/gui_classify_app.py,sha256=Zi15ryc1ocYitRF4kyxlC27XxGyzfSPdvj2d6ZrSh7E,8446
-spacr/gui_core.py,sha256=itgdS6bokEi2ouRMTKjB6T3TnMyUaAPHNTscAEsq4jE,28401
-spacr/gui_elements.py,sha256=IX1Wsh4V1vk3R6ot0CYKgoDgybbd5IcuAGjmst-EpBc,15008
+spacr/gui_core.py,sha256=PmElJrKHtEGYKpGTGgryxxvUvOHMh-wUmhvuHnyI13w,31833
+spacr/gui_elements.py,sha256=b0GJCHyrgJFeqB_IdjkXqMbXeC1reiLyiQ6-MTf_UuQ,73305
 spacr/gui_make_masks_app.py,sha256=tl4M4Q2WQgrrwjRBJVevxJxpNowqzPhWkdCOm2UfRbw,45053
 spacr/gui_make_masks_app_v2.py,sha256=X3izTBXdCZDlkVe-fbG-jmCQtcAbmK0OIivjyWaLhug,30576
 spacr/gui_mask_app.py,sha256=mhTl_XzXLFl8Tx3WYEMpdYB_qw9u5JJa0EdkvlcIzAE,10706
 spacr/gui_measure_app.py,sha256=_C1-XFL5HSquUEEbM_NcxdvHx-socPFCx85MBG4d6xo,10598
 spacr/gui_run.py,sha256=0x85MJqFtREuWuNeIRLB8hFeibKGszfN14POQQWzPDQ,1998
 spacr/gui_sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-spacr/gui_utils.py,sha256=sDPmdXonIiCkXm2NBH_Tghf05_2PPV-ltWY8YCgzOzA,5441
-spacr/gui_wrappers.py,sha256=OBSArqRrM0neEOz44Z_YVceISLqY6WverrVm60GCgqo,4248
+spacr/gui_utils.py,sha256=W0blyZ6JTCBzlkZwXqJpg_uUv41vvqbKvJGCigCeWG8,13890
+spacr/gui_wrappers.py,sha256=-E1SFOmtp7_nfg9QzajI7GJcAcaMug92Pjw7pS1YzjY,4656
 spacr/io.py,sha256=IoERqSwoxJrInYl-E0WfwFOEDZXFdJofk5DmpbyLGWM,112077
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
 spacr/make_masks_app.py,sha256=iGaTwhowoe2JMOSOf8bJwQZTooRhLQx7KO0ewnAmqDY,45138
 spacr/make_masks_app_v2.py,sha256=X3izTBXdCZDlkVe-fbG-jmCQtcAbmK0OIivjyWaLhug,30576
 spacr/mask_app.py,sha256=mhTl_XzXLFl8Tx3WYEMpdYB_qw9u5JJa0EdkvlcIzAE,10706
-spacr/measure.py,sha256=r5nxxULUyka2L5IVdnmEmnMywChY3a4DWGse3ygIh4Q,56000
+spacr/measure.py,sha256=e36NR8raCkvKHZXvTJgPDwObsmsegvc1dAiCqD3oljk,55751
 spacr/measure_app.py,sha256=_C1-XFL5HSquUEEbM_NcxdvHx-socPFCx85MBG4d6xo,10598
 spacr/old_code.py,sha256=jw67DAGoLBd7mWofVzRJSEmCI1Qrff26zIo65SEkV00,13817
-spacr/plot.py,sha256=lrwU51OTWfby1wx73XGyjYmTjLVia7WOmGH5LZZ-4jM,67145
+spacr/plot.py,sha256=DYJEoK1kz2ih6ZGvKiA3xTqeIeKQNhuQKwgrscopFxA,69101
 spacr/sequencing.py,sha256=fHZRnoMSxmhMdadkei3lUeBdckqFyptWdQyWsDW3aaU,83304
-spacr/settings.py,sha256=Yp4VlkmZLuklSbAf3kiIm7iNTWpy2tJuhLNmLUqvFeM,45668
+spacr/settings.py,sha256=CQ93Mb-GjB72yPKcK43jnf22--YRN5kaMYlXwpiRLSc,65699
 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=fxPw9rfikFI0Fha0dLu4h7iCZ2KehwFVJ09ZsiaZhpI,186589
+spacr/utils.py,sha256=OQ8sSBH6VWx2xP_vh4ILJT71B46DFFhsq-Y6WxYdGhI,186891
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model,sha256=z8BbHWZPRnE9D_BHO0fBREE85c1vkltDs-incs2ytXQ,26566572
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv,sha256=fBAGuL_B8ERVdVizO3BHozTDSbZUh1yFzsYK3wkQN68,420
 spacr/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.1.6.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.1.6.dist-info/METADATA,sha256=_Hdz8cTwSC8JIm9le55MysNsudET_JT0gbUjsVRpN44,5049
-spacr-0.1.6.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.1.6.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.1.6.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.1.6.dist-info/RECORD,,
+spacr-0.1.8.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.1.8.dist-info/METADATA,sha256=iOXiNEHaMwhMdS3GpncKdaFEE3xgdoDeK-ndW5eZYdk,5049
+spacr-0.1.8.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.1.8.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.1.8.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.1.8.dist-info/RECORD,,