napari-tmidas 0.3.3__py3-none-any.whl → 0.3.5__py3-none-any.whl

napari_tmidas/_tests/test_skimage_filters.py

@@ -257,3 +257,22 @@ class TestCLAHE:
         assert result_float32.dtype == np.float32
         assert result_float32.max() <= 1.0
         assert result_float32.min() >= 0.0
+
+    def test_clahe_max_workers_parameter(self):
+        """Test that max_workers parameter is respected"""
+        # Create a 4D image that will trigger parallel processing
+        image_4d = np.random.rand(10, 50, 100, 100) * 0.5
+
+        # Test with different worker counts
+        result_1 = equalize_histogram(image_4d, max_workers=1)
+        result_4 = equalize_histogram(image_4d, max_workers=4)
+        result_8 = equalize_histogram(image_4d, max_workers=8)
+
+        # All should produce same shape
+        assert result_1.shape == image_4d.shape
+        assert result_4.shape == image_4d.shape
+        assert result_8.shape == image_4d.shape
+
+        # Results should be nearly identical (some floating point differences are OK)
+        np.testing.assert_allclose(result_1, result_4, rtol=1e-5)
+        np.testing.assert_allclose(result_1, result_8, rtol=1e-5)

napari_tmidas/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.3.3'
-__version_tuple__ = version_tuple = (0, 3, 3)
+__version__ = version = '0.3.5'
+__version_tuple__ = version_tuple = (0, 3, 5)
 
 __commit_id__ = commit_id = None

napari_tmidas/processing_functions/skimage_filters.py

@@ -3,7 +3,6 @@
 Processing functions that depend on scikit-image.
 """
 import concurrent.futures
-import os
 
 import numpy as np
 
@@ -49,10 +48,18 @@ if SKIMAGE_AVAILABLE:
                 "default": 0,
                 "description": "Size of the local region (0 = auto-calculate based on image size). For small features use smaller values (e.g., 32), for large features use larger values (e.g., 128)",
             },
+            "max_workers": {
+                "type": int,
+                "default": 4,
+                "description": "Maximum number of parallel workers (default: 4). Lower values use less memory but are slower. Range: 1-16",
+            },
         },
     )
     def equalize_histogram(
-        image: np.ndarray, clip_limit: float = 0.01, kernel_size: int = 0
+        image: np.ndarray,
+        clip_limit: float = 0.01,
+        kernel_size: int = 0,
+        max_workers: int = 4,
     ) -> np.ndarray:
         """
         Apply CLAHE (Contrast Limited Adaptive Histogram Equalization) to enhance local contrast.
@@ -70,23 +77,29 @@ if SKIMAGE_AVAILABLE:
             Higher values give more contrast but may amplify noise
         kernel_size : int
             Size of the contextual regions (0 = auto-calculate based on image size)
+        max_workers : int
+            Maximum number of parallel workers for processing large datasets (default: 4)
+            Lower values reduce memory usage, higher values increase speed
 
         Returns
         -------
         np.ndarray
             CLAHE-enhanced image with same dtype as input
-        
+
         Notes
         -----
         For large multi-dimensional datasets (TZYX), processing is parallelized across
-        the first dimension to utilize multiple CPU cores effectively.
+        the first dimension to utilize multiple CPU cores effectively. The max_workers
+        parameter controls memory usage vs speed tradeoff.
         """
         # Store original dtype to convert back later
         original_dtype = image.dtype
-        
+
         # Print diagnostic info for multi-dimensional data
         if image.ndim > 2:
-            print(f"Applying CLAHE to {image.ndim}D image with shape {image.shape}")
+            print(
+                f"Applying CLAHE to {image.ndim}D image with shape {image.shape}"
+            )
 
         # Auto-calculate kernel size if not specified
         if kernel_size <= 0:
@@ -99,14 +112,19 @@ if SKIMAGE_AVAILABLE:
         # Ensure kernel_size is odd
         if kernel_size % 2 == 0:
             kernel_size += 1
-        
+
         if image.ndim > 2:
             print(f"Using kernel_size={kernel_size}, clip_limit={clip_limit}")
-        
+
+        # Clamp max_workers to reasonable range
+        max_workers = max(1, min(max_workers, 16))
+
         # For 4D data (TZYX), parallelize across first dimension for better performance
         if image.ndim == 4 and image.shape[0] > 1:
-            print(f"Parallelizing CLAHE across {image.shape[0]} timepoints/slices using {max(1, os.cpu_count() - 1)} workers...")
-            
+            print(
+                f"Parallelizing CLAHE across {image.shape[0]} timepoints/slices using {max_workers} workers..."
+            )
+
             def process_slice(idx):
                 """Process a single slice along first dimension"""
                 result_slice = skimage.exposure.equalize_adapthist(
@@ -115,21 +133,26 @@ if SKIMAGE_AVAILABLE:
                 if (idx + 1) % max(1, image.shape[0] // 10) == 0:
                     print(f"  Processed {idx + 1}/{image.shape[0]} slices")
                 return result_slice
-            
-            # Process in parallel
+
+            # Process in parallel with limited workers to control memory usage
             with concurrent.futures.ThreadPoolExecutor(
-                max_workers=max(1, os.cpu_count() - 1)
+                max_workers=max_workers
             ) as executor:
-                futures = [executor.submit(process_slice, i) for i in range(image.shape[0])]
+                futures = [
+                    executor.submit(process_slice, i)
+                    for i in range(image.shape[0])
+                ]
                 results = [future.result() for future in futures]
-            
+
             result = np.stack(results, axis=0)
             print("CLAHE processing complete!")
-            
+
         elif image.ndim == 3 and image.shape[0] > 5:
             # For 3D data with many slices, also parallelize
-            print(f"Parallelizing CLAHE across {image.shape[0]} slices using {max(1, os.cpu_count() - 1)} workers...")
-            
+            print(
+                f"Parallelizing CLAHE across {image.shape[0]} slices using {max_workers} workers..."
+            )
+
             def process_slice(idx):
                 """Process a single 2D slice"""
                 result_slice = skimage.exposure.equalize_adapthist(
@@ -138,14 +161,17 @@ if SKIMAGE_AVAILABLE:
                 if (idx + 1) % max(1, image.shape[0] // 10) == 0:
                     print(f"  Processed {idx + 1}/{image.shape[0]} slices")
                 return result_slice
-            
-            # Process in parallel
+
+            # Process in parallel with limited workers to control memory usage
             with concurrent.futures.ThreadPoolExecutor(
-                max_workers=max(1, os.cpu_count() - 1)
+                max_workers=max_workers
             ) as executor:
-                futures = [executor.submit(process_slice, i) for i in range(image.shape[0])]
+                futures = [
+                    executor.submit(process_slice, i)
+                    for i in range(image.shape[0])
+                ]
                 results = [future.result() for future in futures]
-            
+
             result = np.stack(results, axis=0)
             print("CLAHE processing complete!")
         else:

{napari_tmidas-0.3.3.dist-info → napari_tmidas-0.3.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-tmidas
-Version: 0.3.3
+Version: 0.3.5
 Summary: A plugin for batch processing of confocal and whole-slide microscopy images of biological tissues
 Author: Marco Meer
 Author-email: marco.meer@pm.me
@@ -161,7 +161,8 @@ Then find napari-tmidas in the **Plugins** menu. [Watch video tutorials →](htt
 
 - [Batch Crop Anything](docs/crop_anything.md) - Interactive object cropping with SAM2
 - [Batch Label Inspection](docs/batch_label_inspection.md) - Manual label verification and editing
-- [Advanced Filters](docs/advanced_processing.md) - SciPy/scikit-image filters
+- [SciPy Filters](docs/advanced_processing.md#scipy-filters) - Gaussian, median, morphological operations
+- [Scikit-Image Filters](docs/advanced_processing.md#scikit-image-filters) - CLAHE, thresholding, edge detection
 
 ## 💻 Installation
 

{napari_tmidas-0.3.3.dist-info → napari_tmidas-0.3.5.dist-info}/RECORD

@@ -10,7 +10,7 @@ napari_tmidas/_registry.py,sha256=yunbEoDe1JZREMab4BeP7wka17IwK1toV5g1imju30c,21
 napari_tmidas/_roi_colocalization.py,sha256=0ZSs7JlJKPhGibnETf6Rj746T3YV4AUgynWmZbmNjHw,92257
 napari_tmidas/_sample_data.py,sha256=khuv1jemz_fCjqNwEKMFf83Ju0EN4S89IKydsUMmUxw,645
 napari_tmidas/_ui_utils.py,sha256=wBmaR-3wdgizb234atsjUU2DElsM5-tf4TIsxGLaHzI,1499
-napari_tmidas/_version.py,sha256=lemL_4Kl75FgrO6lVuFrrtw6-Dcf9wtXBalKkXuzkO4,704
+napari_tmidas/_version.py,sha256=UAb2Toi6SAdScDfq1uKRRv5QpMUuRtJqqwNxTMGe5Q4,704
 napari_tmidas/_widget.py,sha256=Uab5WuJK2fgdlGga6iNnHsiZjRMUq2KM3u0N5JJW8DA,5495
 napari_tmidas/_writer.py,sha256=wbVfHFjjHdybSg37VR4lVmL-kdCkDZsUPDJ66AVLaFQ,1941
 napari_tmidas/napari.yaml,sha256=1Am1dA0-ZtCXk6veIT6jrMz3zwQ7dF8_p9tZTFx_vTg,2641
@@ -28,7 +28,7 @@ napari_tmidas/_tests/test_regionprops_analysis.py,sha256=IGAEtdg83R9aH8wsINR8VCv
 napari_tmidas/_tests/test_registry.py,sha256=0dVpeGE273YDPDy6KMInfkz2JAaJ_SUKFOySKn160_c,4795
 napari_tmidas/_tests/test_sample_data.py,sha256=D1HU_C3hWpO3mlSW_7Z94xaYHDtxz0XUrMjQoYop9Ag,104
 napari_tmidas/_tests/test_scipy_filters.py,sha256=SUcgyFh2IY4YVJvVO6_J1JdgkCsYdW36RgpHLkkp2vg,6268
-napari_tmidas/_tests/test_skimage_filters.py,sha256=TgvwcE_1kpdRzg5Hex9z9IoJc5Mt7IJjbpsdmZFiOGc,9869
+napari_tmidas/_tests/test_skimage_filters.py,sha256=yj0DrfOYyyyjNps3Yzvwwh_wtR4Mmz4_L5DNjFNBbSs,10739
 napari_tmidas/_tests/test_split_channels.py,sha256=aMvjppoHlPAuwWLGYa1UcfBM_fvu0zM7Elam5JWaAQw,7448
 napari_tmidas/_tests/test_spotiflow.py,sha256=BLSaD8z8r2zbkYEGmfQ3JkSgw5OkvEORnSzpbkIIz4Y,2578
 napari_tmidas/_tests/test_tyx_display_fix.py,sha256=rhKbmM1rkPAAUeV3x3VuJkzXwEoqgi3Gtrxi1PP4ijs,4804
@@ -51,16 +51,16 @@ napari_tmidas/processing_functions/regionprops_analysis.py,sha256=ySmzlY_F8uXWQI
 napari_tmidas/processing_functions/sam2_env_manager.py,sha256=w-X493XdHWAE8UhyHhEEVJ3uvLi2VdS-UFU7yPqnagg,2569
 napari_tmidas/processing_functions/sam2_mp4.py,sha256=lEdrqQP36_kw2g3soyu81CCRXCkI5DdSExfq5Bc5kig,11523
 napari_tmidas/processing_functions/scipy_filters.py,sha256=1Y69F5Pe-MEJPwQEs_6Ci3ncFuTKiRAuKRvDxmOQUPw,17871
-napari_tmidas/processing_functions/skimage_filters.py,sha256=og2mrEHNLBGQA6j07DHX94rhXJs4fRt5nzjpLyUmbeM,28154
+napari_tmidas/processing_functions/skimage_filters.py,sha256=dLEKw8Nw9-9b6hbPLebifmYj6l5x7KeA28DthWaMBP0,28920
 napari_tmidas/processing_functions/spotiflow_detection.py,sha256=2FLnDNXLc0eNj8vhp_XBv_bukX5pJOEhuiyXbUzzcyU,32811
 napari_tmidas/processing_functions/spotiflow_env_manager.py,sha256=07J_tYADMvIVIr_afniSNt8uEduecqpNblSWEj9aH7Q,20323
 napari_tmidas/processing_functions/timepoint_merger.py,sha256=7pXyfcI2rXZz6_TP3v_WejmMFivNVyUzkzBmifMiFKA,27424
 napari_tmidas/processing_functions/trackastra_tracking.py,sha256=IkFk5HoEZmKdcu5jXri4WMhHN1KTADDMxSpeYfPgSbo,9976
 napari_tmidas/processing_functions/viscy_env_manager.py,sha256=eJ9NsyrtypvxRAFVir9n9RtKaaj6GTpIrOFNLScoVDY,11999
 napari_tmidas/processing_functions/viscy_virtual_staining.py,sha256=Aa__YweYzSFYUTkbneDZ2lxRBplozrQvXGSiMFzUhA4,12422
-napari_tmidas-0.3.3.dist-info/licenses/LICENSE,sha256=tSjiOqj57exmEIfP2YVPCEeQf0cH49S6HheQR8IiY3g,1485
-napari_tmidas-0.3.3.dist-info/METADATA,sha256=aahB9CKda7grLnpGSUtqS9B-SrP1qrhOPg_0Rp_CSMo,10348
-napari_tmidas-0.3.3.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-napari_tmidas-0.3.3.dist-info/entry_points.txt,sha256=fbVjzbJTm4aDMIBtel1Lyqvq-CwXY7wmCOo_zJ-jtRY,60
-napari_tmidas-0.3.3.dist-info/top_level.txt,sha256=63ybdxCZ4SeT13f_Ou4TsivGV_2Gtm_pJOXToAt30_E,14
-napari_tmidas-0.3.3.dist-info/RECORD,,
+napari_tmidas-0.3.5.dist-info/licenses/LICENSE,sha256=tSjiOqj57exmEIfP2YVPCEeQf0cH49S6HheQR8IiY3g,1485
+napari_tmidas-0.3.5.dist-info/METADATA,sha256=-wGsfY5Pn_4fJPeF5Y8dCNnGnw-0kSDQe-vLVWKzvcQ,10488
+napari_tmidas-0.3.5.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+napari_tmidas-0.3.5.dist-info/entry_points.txt,sha256=fbVjzbJTm4aDMIBtel1Lyqvq-CwXY7wmCOo_zJ-jtRY,60
+napari_tmidas-0.3.5.dist-info/top_level.txt,sha256=63ybdxCZ4SeT13f_Ou4TsivGV_2Gtm_pJOXToAt30_E,14
+napari_tmidas-0.3.5.dist-info/RECORD,,