spacr 0.1.55__py3-none-any.whl → 0.1.62__py3-none-any.whl

spacr/gui_wrappers.py

@@ -0,0 +1,137 @@
+import traceback, matplotlib, spacr
+import matplotlib.pyplot as plt
+matplotlib.use('Agg')
+
+fig_queue = None
+
+def my_show():
+    """
+    Replacement for plt.show() that queues figures instead of displaying them.
+    """
+    fig = plt.gcf()
+    fig_queue.put(fig)
+    plt.close(fig)
+
+def measure_crop_wrapper(settings, q, fig_queue):
+    """
+    Wraps the measure_crop function to integrate with GUI processes.
+    
+    Parameters:
+    - settings: dict, The settings for the measure_crop function.
+    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
+    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
+    """
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        print('start')
+        spacr.measure.measure_crop(settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)
+        traceback.print_exc()
+    finally:
+        plt.show = original_show  
+        
+def preprocess_generate_masks_wrapper(settings, q, fig_queue):
+    """
+    Wraps the measure_crop function to integrate with GUI processes.
+    
+    Parameters:
+    - settings: dict, The settings for the measure_crop function.
+    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
+    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
+    """
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        spacr.core.preprocess_generate_masks(src=settings['src'], settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)
+        traceback.print_exc()
+    finally:
+        plt.show = original_show
+
+def sequencing_wrapper(settings, q, fig_queue):
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        spacr.sequencing.analyze_reads(settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)
+        traceback.print_exc()
+    finally:
+        plt.show = original_show
+
+def umap_wrapper(settings, q, fig_queue):
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        spacr.core.generate_image_umap(settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)
+        traceback.print_exc()
+    finally:
+        plt.show = original_show
+
+def train_test_model_wrapper(settings, q, fig_queue):
+    """
+    Wraps the measure_crop function to integrate with GUI processes.
+    
+    Parameters:
+    - settings: dict, The settings for the measure_crop function.
+    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
+    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
+    """
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        spacr.core.train_test_model(settings['src'], settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)  # Send the error message to the GUI via the queue
+        traceback.print_exc()
+    finally:
+        plt.show = original_show  # Restore the original plt.show function
+        
+        
+def run_multiple_simulations_wrapper(settings, q, fig_queue):
+    """
+    Wraps the run_multiple_simulations function to integrate with GUI processes.
+    
+    Parameters:
+    - settings: dict, The settings for the run_multiple_simulations function.
+    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
+    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
+    """
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        spacr.sim.run_multiple_simulations(settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)  # Send the error message to the GUI via the queue
+        traceback.print_exc()
+    finally:
+        plt.show = original_show  # Restore the original plt.show function

spacr/measure.py

@@ -16,12 +16,6 @@ from skimage.util import img_as_bool
 
 from .logger import log_function_call
 
-#from .io import create_database, _save_settings_to_db
-#from .timelapse import _timelapse_masks_to_gif, _scmovie
-#from .plot import _plot_cropped_arrays, _save_scimg_plot
-#from .utils import _merge_overlapping_objects, _filter_object, _relabel_parent_with_child_labels, _exclude_objects
-#from .utils import _merge_and_save_to_database, _crop_center, _find_bounding_box, _generate_names, _get_percentiles, normalize_to_dtype, _map_wells_png, _list_endpoint_subdirectories, _generate_representative_images
-
 def get_components(cell_mask, nucleus_mask, pathogen_mask):
     """
     Get the components (nucleus and pathogens) for each cell in the given masks.
@@ -626,8 +620,13 @@ def _measure_crop_core(index, time_ls, file, settings):
 
         file_name = os.path.splitext(file)[0]
         data = np.load(os.path.join(settings['input_folder'], file))
-
         data_type = data.dtype
+        if data_type not in ['uint8','uint16']:
+            data_type_before = data_type
+            data = data.astype(np.uint16)
+            data_type = data.dtype
+            print(f'Converted data from {data_type_before} to {data_type}')
+
         if settings['save_measurements']:
             os.makedirs(source_folder+'/measurements', exist_ok=True)
             _create_database(source_folder+'/measurements/measurements.db')    
@@ -832,7 +831,6 @@ def _measure_crop_core(index, time_ls, file, settings):
                                     png_channels = normalize_to_dtype(png_channels, settings['normalize'][0], settings['normalize'][1], percentile_list=percentile_list)
                             else:
                                 png_channels = normalize_to_dtype(png_channels, 0, 100)
-
                             os.makedirs(png_folder, exist_ok=True)
 
                             if png_channels.shape[2] == 2:

spacr/plot.py

@@ -1565,4 +1565,56 @@ def plot_feature_importance(feature_importance_df):
     ax.set_xlabel('Feature Importance', fontsize=font_size)
     ax.tick_params(axis='both', which='major', labelsize=font_size)
     plt.tight_layout()
-    return fig
+    return fig
+
+def read_and_plot__vision_results(base_dir, y_axis='accuracy', name_split='_time', y_lim=[0.8, 0.9]):
+    # List to store data from all CSV files
+    data_frames = []
+
+    dst = os.path.join(base_dir, 'result')
+    os.mkdir(dst,exists=True)
+
+    # Walk through the directory
+    for root, dirs, files in os.walk(base_dir):
+        for file in files:
+            if file.endswith("_test_result.csv"):
+                file_path = os.path.join(root, file)
+                # Extract model information from the file name
+                file_name = os.path.basename(file_path)
+                model = file_name.split(f'{name_split}')[0]
+                
+                # Extract epoch information from the file name
+                epoch_info = file_name.split('_time')[1]
+                base_folder = os.path.dirname(file_path)
+                epoch = os.path.basename(base_folder)
+                
+                # Read the CSV file
+                df = pd.read_csv(file_path)
+                df['model'] = model
+                df['epoch'] = epoch
+                
+                # Append the data frame to the list
+                data_frames.append(df)
+    
+    # Concatenate all data frames
+    if data_frames:
+        result_df = pd.concat(data_frames, ignore_index=True)
+        
+        # Calculate average y_axis per model
+        avg_metric = result_df.groupby('model')[y_axis].mean().reset_index()
+        avg_metric = avg_metric.sort_values(by=y_axis)
+        print(avg_metric)
+        
+        # Plotting the results
+        plt.figure(figsize=(10, 6))
+        plt.bar(avg_metric['model'], avg_metric[y_axis])
+        plt.xlabel('Model')
+        plt.ylabel(f'{y_axis}')
+        plt.title(f'Average {y_axis.capitalize()} per Model')
+        plt.xticks(rotation=45)
+        plt.tight_layout()
+        if y_lim is not None:
+            plt.ylim(y_lim)
+        plt.show()
+    else:
+        print("No CSV files found in the specified directory.")

spacr/settings.py

@@ -795,7 +795,8 @@ def check_settings(vars_dict):
     return settings
 
 def generate_fields(variables, scrollable_frame):
-    from .gui_utils import create_input_field, spacrToolTip
+    from .gui_utils import create_input_field
+    from .gui_elements import spacrToolTip
     row = 1
     vars_dict = {}
     tooltips = {

spacr/utils.py

@@ -1,4 +1,4 @@
-import sys, os, re, sqlite3, torch, torchvision, random, string, shutil, cv2, tarfile, glob
+import sys, os, re, sqlite3, torch, torchvision, random, string, shutil, cv2, tarfile, glob, psutil, platform, signal
 
 import numpy as np
 from cellpose import models as cp_models
@@ -72,13 +72,12 @@ from sklearn.cluster import KMeans
 from scipy import stats
 
 from .logger import log_function_call
-
-import os
-import signal
-import psutil
-import platform
 from multiprocessing import set_start_method, get_start_method
 
+import tkinter as tk
+from tkinter import ttk
+import tkinter.font as tkFont
+
 def reset_mp():
     current_method = get_start_method()
     system = platform.system()
@@ -473,7 +472,7 @@ 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.
 
@@ -492,7 +491,16 @@ 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)
 
@@ -4051,7 +4059,7 @@ 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):
 
@@ -4091,7 +4099,7 @@ 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)
@@ -4383,4 +4391,4 @@ def correct_masks(src):
 
     cell_path = os.path.join(src,'norm_channel_stack', 'cell_mask_stack')
     convert_and_relabel_masks(cell_path)
-    _load_and_concatenate_arrays(src, [0,1,2,3], 1, 0, 2)
+    _load_and_concatenate_arrays(src, [0,1,2,3], 1, 0, 2)

{spacr-0.1.55.dist-info → spacr-0.1.62.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.55
+Version: 0.1.62
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.1.55.dist-info → spacr-0.1.62.dist-info}/RECORD

@@ -1,11 +1,11 @@
-spacr/__init__.py,sha256=cHMZ6CcoOfm_3igLgndH3hxDbW8kBx5pqM04zEtlg3w,1339
+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=lnjVLwzwpZ9-5cHuEgCmAC-pAnGQmmWyjTXDF0NV2Ps,23560
+spacr/app_annotate.py,sha256=QKWQ0GGiKu5ik14OB4Z3YIqIJYpmsNJlqpnfnQPowAM,23563
 spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
-spacr/app_make_masks.py,sha256=0qbZhCnWzqJAhRGCI4j7GdJx8mEBA8j7LxGjWlQHyss,45060
+spacr/app_make_masks.py,sha256=0N8Wfby3HaVX4m9tOyBy7OQolamYG9lVwmnlzkK4uaE,44993
 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
@@ -14,43 +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/core.py,sha256=JZ8LerUgXarhCQWsUlBD6KULhsIBDlpvotZCSwRt1rI,160317
 spacr/deep_spacr.py,sha256=rvqOoY9dadcTcKiABf61Nb8HEMVp1NouFmtAE2ee1T4,37056
 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=awunZePAu-LH-rPEUhxVTAXXkG5L8oyHz-qHcEX6Im4,7765
+spacr/gui.py,sha256=kvQ0X9nyZz_BWsOyJSNSv7gEG1ZuTqjz4EH78e0uul4,7783
 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=WoDrxZg8bzIw5G-WsXG4ek-62cMsU6z0zyn_1P9CX7E,15063
 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=8joqzUdN_26VeI2Gsd0Tjh_ArAFzjE323VGSHDJnev4,51624
+spacr/gui_utils.py,sha256=sDPmdXonIiCkXm2NBH_Tghf05_2PPV-ltWY8YCgzOzA,5441
+spacr/gui_wrappers.py,sha256=OBSArqRrM0neEOz44Z_YVceISLqY6WverrVm60GCgqo,4248
 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=C8el2DFz1xMa8_V5xU2q5QHs-aZzfCniI-ylcY5RYSI,55736
 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=1tcgdn4RWbX7_Qto0nHDP_f202sT7d_9-UU_W-q8cPc,45639
+spacr/settings.py,sha256=Yp4VlkmZLuklSbAf3kiIm7iNTWpy2tJuhLNmLUqvFeM,45668
 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=MM31yWquNDFmhxAU3l3Qx64peQJ6VWOuNGS6gkia5AY,186541
+spacr/utils.py,sha256=149Bbha9OXAKyDwABgHz5h4O7Gqy6aeFLA1pMSq311s,186966
 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-0.1.55.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.1.55.dist-info/METADATA,sha256=uTrkXO1JPmHgXWuuZJzsd8LQCWkoY0qrIBfkMGymzQE,5050
-spacr-0.1.55.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.1.55.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.1.55.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.1.55.dist-info/RECORD,,
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