miblab-plot 0.0.9__tar.gz → 0.0.11__tar.gz

{miblab_plot-0.0.9/src/miblab_plot.egg-info → miblab_plot-0.0.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: miblab-plot
-Version: 0.0.9
+Version: 0.0.11
 Summary: Plotting utilities for medical images
 Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>
 License-Expression: Apache-2.0
@@ -26,7 +26,6 @@ Requires-Dist: imageio
 Requires-Dist: zarr
 Requires-Dist: pillow
 Requires-Dist: dbdicom
-Requires-Dist: miblab_ssa
 Dynamic: license-file
 
 # miblab-plot

{miblab_plot-0.0.9 → miblab_plot-0.0.11}/pyproject.toml

@@ -6,7 +6,7 @@ requires = ['setuptools>=61.2']
 
 [project]
 name = "miblab-plot"
-version = "0.0.9"
+version = "0.0.11"
 dependencies = [
     "numpy",
     "matplotlib",
@@ -18,7 +18,6 @@ dependencies = [
     "zarr",
     "pillow",
     "dbdicom",
-    "miblab_ssa",
 ]
 
 # optional information

{miblab_plot-0.0.9 → miblab_plot-0.0.11}/src/miblab_plot/__init__.py

@@ -2,5 +2,6 @@ from .image_3d import (
     volume_to_mosaic, 
     mosaic_overlay, 
     mosaic_checkerboard,
+    db_mosaic,
 )
 from . import mp4, pvplot, gui

{miblab_plot-0.0.9 → miblab_plot-0.0.11}/src/miblab_plot/image_3d.py

@@ -6,9 +6,67 @@ import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 from tqdm import tqdm
+import dbdicom as db
 
 
 
+def db_mosaic(series_to_display, pngfile, title="Center slices"):
+
+    # Build list of center slices
+    center_slices = []
+    for series in tqdm(series_to_display, desc='Reading center images'):
+        vol = db.volume(series, verbose=0)
+        center_slice = vol.values[:,:,round(vol.shape[-1]/2)]
+        center_slices.append(center_slice)
+
+    # Display center slices as mosaic
+    n_imgs = len(center_slices)
+    aspect_ratio = 16/9
+    nrows = int(np.ceil(np.sqrt(n_imgs / aspect_ratio)))
+    ncols = int(np.ceil(aspect_ratio * nrows))
+    fig, ax = plt.subplots(nrows=nrows, ncols=ncols, gridspec_kw = {'wspace':0, 'hspace':0}, figsize=(ncols, nrows), dpi=300)
+
+    i=0
+    for row in tqdm(ax, desc='Building png'):
+        for col in row:
+
+            col.set_xticklabels([])
+            col.set_yticklabels([])
+            col.set_aspect('equal')
+            col.axis("off")
+
+            if i < len(center_slices):
+
+                # Show center image
+                col.imshow(
+                    center_slices[i].T, 
+                    cmap='gray', 
+                    interpolation='none', 
+                    vmin=0, 
+                    vmax=np.mean(center_slices[i]) + 2 * np.std(center_slices[i])
+                )
+                # Add white text with black background in upper-left corner
+                patient_id = series_to_display[i][1]
+                series_desc = series_to_display[i][-1][0]
+                study = series_to_display[i][2][0]
+                col.text(
+                    0.01, 0.99,                   
+                    f'{patient_id}_{study}\n{series_desc}',   
+                    color='white',
+                    fontsize=2,
+                    ha='left',
+                    va='top',
+                    transform=col.transAxes,     # Use axes coordinates
+                    bbox=dict(facecolor='black', alpha=0.7, boxstyle='round,pad=0.3')
+                )
+
+            i+=1 
+
+    fig.suptitle(title, fontsize=14)
+    fig.savefig(pngfile)
+    plt.close()
+    
+
 def get_distinct_colors(rois, colormap='jet', opacity=0.6):
     if len(rois)==1:
         colors = [[1, 0, 0, opacity]]
@@ -165,6 +223,7 @@ def mosaic_overlay(
         vmin=None,
         vmax=None,
         opacity=0.6,
+        colors=None
     ):
 
     # Set defaults color window
@@ -174,7 +233,8 @@ def mosaic_overlay(
         vmax=np.mean(img) + 2 * np.std(img)
 
     # Define RGBA colors (R, G, B, Alpha) — alpha controls transparency
-    colors = get_distinct_colors(rois, colormap=colormap, opacity=opacity)
+    if colors is None:
+        colors = get_distinct_colors(rois, colormap=colormap, opacity=opacity)
 
     # Get all masks as boolean arrays
     masks = [m.astype(bool) for m in rois.values()]

{miblab_plot-0.0.9 → miblab_plot-0.0.11}/src/miblab_plot/pvplot.py

@@ -8,8 +8,6 @@ import pyvista as pv
 import dbdicom as db
 import zarr
 
-import miblab_ssa as ssa
-
 
 def setup_rendering_env():
 
@@ -68,7 +66,7 @@ def mosaic_masks_dcm(masks, imagefile, labels=None, view_vector=(1, 0, 0)):
 
         # Load data
         vol = db.volume(mask_series, verbose=0)
-        mask_norm = ssa.sdf_ft.smooth_mask(vol.values, order=32)
+        mask_norm = vol.values
 
         # Plot tile
         orig_vol = pv.wrap(mask_norm.astype(float))
@@ -202,8 +200,7 @@ def multiple_mosaic_masks_da(masks: list, directions: dict, labels, columns=None
     
     surfaces = []
     for mask_series in tqdm(masks, desc="Pre-calculating Surfaces"):
-        # Your Spline/RBF smoothing
-        #mask_norm = ssa.sdf_ft.smooth_mask(mask_series[:].astype(bool), order=16)
+        
         mask_norm = mask_series[:].astype(bool)
         
         vol = pv.wrap(mask_norm.astype(np.float32))
@@ -327,7 +324,7 @@ def multiple_mosaic_masks_npz(masks, directions:dict, labels, columns=None, rows
 
         # Load data once
         vol = db.npz.volume(mask_series)
-        mask_norm = ssa.sdf_ft.smooth_mask(vol.values.astype(bool), order=32)
+        mask_norm = vol.values.astype(bool)
 
         orig_vol = pv.wrap(mask_norm.astype(float))
         orig_vol.spacing = [1.0, 1.0, 1.0]
@@ -443,7 +440,7 @@ def mosaic_masks_npz(masks, imagefile, labels=None, view_vector=(1, 0, 0)):
 
         # Load data
         vol = db.npz.volume(mask_series)
-        mask_norm = ssa.sdf_ft.smooth_mask(vol.values.astype(bool), order=32)
+        mask_norm = vol.values.astype(bool)
 
         # Plot tile
         orig_vol = pv.wrap(mask_norm.astype(float))
@@ -456,53 +453,3 @@ def mosaic_masks_npz(masks, imagefile, labels=None, view_vector=(1, 0, 0)):
     plotter.screenshot(imagefile)
     plotter.close()
 
-
-def mosaic_features_npz(features, imagefile, labels=None, view_vector=(1, 0, 0)):
-
-    # Plot settings
-    aspect_ratio = 16/9
-    width = 150
-    height = 150
-
-    # Count nr of mosaics
-    n_mosaics = len(features)
-    nrows = int(np.ceil(np.sqrt((width*n_mosaics)/(aspect_ratio*height))))
-    ncols = int(np.ceil(n_mosaics/nrows))
-
-    plotter = pv.Plotter(
-        window_size=(ncols*width, nrows*height), 
-        shape=(nrows, ncols), 
-        border=False, 
-        # off_screen=True,
-        off_screen=pv.OFF_SCREEN,
-    )
-    plotter.background_color = 'white'
-
-    row = 0
-    col = 0
-    for i, feat in tqdm(enumerate(features), desc=f'Building mosaic'):
-
-        # Set up plotter
-        plotter.subplot(row,col)
-        if labels is not None:
-            plotter.add_text(labels[i], font_size=6)
-        if col == ncols-1:
-            col = 0
-            row += 1
-        else:
-            col += 1
-
-        # Load data
-        ft = np.load(feat)
-        mask_norm = ssa.sdf_ft.mask_from_features(ft['features'], ft['shape'], ft['order'])
-
-        # Plot tile
-        orig_vol = pv.wrap(mask_norm.astype(float))
-        orig_vol.spacing = [1.0, 1.0, 1.0]
-        orig_surface = orig_vol.contour(isosurfaces=[0.5])
-        plotter.add_mesh(orig_surface, color='lightblue', opacity=1.0, style='surface')
-        plotter.camera_position = 'iso'
-        plotter.view_vector(view_vector)  # rotate 180° around vertical axis
-    
-    plotter.screenshot(imagefile)
-    plotter.close()

{miblab_plot-0.0.9 → miblab_plot-0.0.11/src/miblab_plot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: miblab-plot
-Version: 0.0.9
+Version: 0.0.11
 Summary: Plotting utilities for medical images
 Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>
 License-Expression: Apache-2.0
@@ -26,7 +26,6 @@ Requires-Dist: imageio
 Requires-Dist: zarr
 Requires-Dist: pillow
 Requires-Dist: dbdicom
-Requires-Dist: miblab_ssa
 Dynamic: license-file
 
 # miblab-plot

{miblab_plot-0.0.9 → miblab_plot-0.0.11}/src/miblab_plot.egg-info/requires.txt

@@ -8,4 +8,3 @@ imageio
 zarr
 pillow
 dbdicom
-miblab_ssa