miblab-plot 0.0.1__py3-none-any.whl → 0.0.2__py3-none-any.whl

miblab_plot/__init__.py

@@ -1 +1,5 @@
-from miblab_plot.image_3d import volume_to_mosaic, mosaic_overlay
+from miblab_plot.image_3d import (
+    volume_to_mosaic, 
+    mosaic_overlay, 
+    mosaic_checkerboard,
+)

miblab_plot/image_3d.py

@@ -1,9 +1,6 @@
 from math import ceil
 
 from PIL import Image
-import numpy as np
-
-
 import numpy as np
 import matplotlib
 matplotlib.use('Agg')
@@ -12,31 +9,162 @@ from tqdm import tqdm
 
 
 
-def get_distinct_colors(rois, colormap='jet'):
+def get_distinct_colors(rois, colormap='jet', opacity=0.6):
     if len(rois)==1:
-        colors = [[1, 0, 0, 0.6]]
+        colors = [[1, 0, 0, opacity]]
     elif len(rois)==2:
-        colors = [[1, 0, 0, 0.6], [0, 1, 0, 0.6]]
+        colors = [[1, 0, 0, opacity], [0, 1, 0, opacity]]
     elif len(rois)==3:
-        colors = [[1, 0, 0, 0.6], [0, 1, 0, 0.6], [0, 0, 1, 0.6]]
+        colors = [[1, 0, 0, opacity], [0, 1, 0, opacity], [0, 0, 1, opacity]]
     else:
         n = len(rois)
         #cmap = cm.get_cmap(colormap, n)
         cmap = matplotlib.colormaps[colormap]
-        colors = [cmap(i)[:3] + (0.6,) for i in np.linspace(0, 1, n)]  # Set alpha to 0.6 for transparency
+        colors = [cmap(i)[:3] + (opacity,) for i in np.linspace(0, 1, n)]
 
     return colors
 
 
+def mosaic_checkerboard(fixed, coreg, file, normalize=False, square_size=32, aspect_ratio=1.8, vmin=None, vmax=None):
+
+    fixed = np.array(fixed)
+    coreg = np.array(coreg)
+
+    if fixed.shape != coreg.shape:
+        raise ValueError("Input arrays must have the same shape")
+    
+    if normalize:
+        fixed = _normalize(fixed)
+        coreg = _normalize(coreg)
+        # fixed = (fixed - fixed.min()) / (fixed.max() - fixed.min())
+        # coreg = (coreg - coreg.min()) / (coreg.max() - coreg.min())
+
+    # Set defaults color window
+    if vmin is None:
+        vmin=np.percentile(np.concatenate([fixed, coreg]), 5)
+    if vmax is None:
+        vmax=np.percentile(np.concatenate([fixed, coreg]), 95)
+
+    # Determine number of rows and columns
+    # c*r = n -> c=n/r
+    # c*w / r*h = a -> w*n/r = a*r*h -> (w*n) / (a*h) = r**2
+    width = fixed.shape[0]
+    height = fixed.shape[1]
+    n_mosaics = fixed.shape[2]
+    nrows = int(np.round(np.sqrt((width*n_mosaics)/(aspect_ratio*height))))
+    ncols = int(np.ceil(n_mosaics/nrows))
+
+    # Set up figure 
+    fig, ax = plt.subplots(
+        nrows=nrows, 
+        ncols=ncols, 
+        gridspec_kw = {'wspace':0, 'hspace':0}, 
+        figsize=(ncols*width/max([width,height]), nrows*height/max([width,height])),
+        dpi=300,
+    )
+    plt.subplots_adjust(left=0, right=1, top=1, bottom=0)
+
+    # Build figure
+    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")
+
+            # Display the background image
+            if i < n_mosaics:
+                img = checkerboard(fixed[:,:,i], coreg[:,:,i], square_size)
+                col.imshow(
+                    img.T, 
+                    cmap='gray', 
+                    interpolation='none', 
+                    vmin=vmin, 
+                    vmax=vmax,
+                )
+
+            i += 1
+
+    # fig.suptitle('Mask overlay', fontsize=14)
+    fig.savefig(file, bbox_inches='tight', pad_inches=0)
+    plt.close()
+
+
+
+def _normalize(x: np.ndarray) -> np.ndarray:
+    """
+    Normalize an array so that median = 0 and IQR = 1.
+
+    Parameters
+    ----------
+    x : np.ndarray
+        Input array (any shape)
+
+    Returns
+    -------
+    np.ndarray
+        Normalized array
+    """
+    x = np.asarray(x, dtype=float)
+
+    q25, q50, q75 = np.percentile(x, [25, 50, 75])
+    iqr = q75 - q25
+
+    if iqr == 0:
+        raise ValueError("IQR is zero; cannot normalize")
+
+    return (x - q50) / iqr
+
+
+
+def checkerboard(fixed: np.ndarray, coreg: np.ndarray, square_size: int) -> np.ndarray:
+    """
+    Creates a checkerboard pattern from two 2D arrays.
+
+    Parameters
+    ----------
+    fixed : np.ndarray
+        The first 2D array (e.g., fixed image)
+    coreg : np.ndarray
+        The second 2D array (e.g., coregistered image)
+        Must have the same shape as `fixed`.
+    square_size : int
+        The size of each checkerboard square in pixels.
+
+    Returns
+    -------
+    np.ndarray
+        Checkerboard array combining `fixed` and `coreg`.
+    """
+    if fixed.shape != coreg.shape:
+        raise ValueError("Input arrays must have the same shape")
+    
+    rows, cols = fixed.shape
+    
+    # Create a boolean checkerboard mask
+    row_blocks = np.arange(rows) // square_size
+    col_blocks = np.arange(cols) // square_size
+    mask = (row_blocks[:, None] + col_blocks[None, :]) % 2 == 0  # True = use fixed
+    
+    # Build the checkerboard
+    checker = np.where(mask, fixed, coreg)
+    
+    return checker
+
+
+
 def mosaic_overlay(
         img, 
         rois, 
         file, 
         colormap='tab20', 
-        aspect_ratio=16/9, 
+        aspect_ratio=1.8, 
         margin=None,
         vmin=None,
         vmax=None,
+        opacity=0.6,
     ):
 
     # Set defaults color window
@@ -46,7 +174,7 @@ 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)
+    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-0.0.1.dist-info → miblab_plot-0.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: miblab-plot
-Version: 0.0.1
+Version: 0.0.2
 Summary: Plotting utilities for medical images
 Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>
 License-Expression: Apache-2.0

miblab_plot-0.0.2.dist-info/RECORD

@@ -0,0 +1,7 @@
+miblab_plot/__init__.py,sha256=7k0ANRoyjRqb-6xxqpbR657tOMBf5UtLmtBif_PC93s,109
+miblab_plot/image_3d.py,sha256=nwP_cF--H_rUSrL-Ozp6qzbO-4Y8159TkWOsg27s5b0,10779
+miblab_plot-0.0.2.dist-info/licenses/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
+miblab_plot-0.0.2.dist-info/METADATA,sha256=vAnLpEphCq9CTiEX5JkUONETakTH2ElVgr88HAXBHyg,937
+miblab_plot-0.0.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+miblab_plot-0.0.2.dist-info/top_level.txt,sha256=w6glSbOeiZvvL3Tywi8XTJxYAatD7VMkOifD5iKnTSU,12
+miblab_plot-0.0.2.dist-info/RECORD,,

miblab_plot-0.0.1.dist-info/RECORD

@@ -1,7 +0,0 @@
-miblab_plot/__init__.py,sha256=rXyuHtEzmdjmiXdm-0ZURw1DxO_W70UDd0OxY9nKxO4,65
-miblab_plot/image_3d.py,sha256=Nah2J8QjWV9YsF9SSwaicSQJCPDaio0MS8aIEduCG1I,7035
-miblab_plot-0.0.1.dist-info/licenses/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
-miblab_plot-0.0.1.dist-info/METADATA,sha256=xjCti8UCrj_gP7mPzIyTEPydXJWwuVTD5aVUmBjL68Q,937
-miblab_plot-0.0.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-miblab_plot-0.0.1.dist-info/top_level.txt,sha256=w6glSbOeiZvvL3Tywi8XTJxYAatD7VMkOifD5iKnTSU,12
-miblab_plot-0.0.1.dist-info/RECORD,,