Update for image handling with odd dimensions

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

Author: ericspod

Dockerfile

@@ -10,7 +10,7 @@ FROM alpine:3.20
 RUN apk update && \
     apk add py3-qt5 py3-numpy py3-pip py3-pillow ttf-freefont mesa-dri-gallium && \
     rm -rf /var/cache/apk/* usr/lib/python3.12/EXTERNALLY-MANAGED &&\
-    pip3 install pydicom pyqtgraph
+    pip3 install pydicom pyqtgraph pylibjpeg
 
 
 WORKDIR /dicombrowser

dicombrowser/__init__.py

@@ -17,6 +17,5 @@
 # with this program (LICENSE.txt).  If not, see <http://www.gnu.org/licenses/>
 
 
-
 from ._version import __version__, __author__, __copyright__
 from .dicombrowser import mainargv

dicombrowser/_version.py

@@ -17,9 +17,8 @@
 # with this program (LICENSE.txt).  If not, see <http://www.gnu.org/licenses/>
 
 __appname__ = "DicomBrowser"
-__version_info__ = (1, 5, 0)  # global application version, major/minor/patch
+__version_info__ = (1, 5, 1)  # global application version, major/minor/patch
 __version__ = f"{__version_info__[0]}.{__version_info__[1]}.{__version_info__[2]}"
 __author__ = "Eric Kerfoot"
-__author_email__="eric.kerfoot@kcl.ac.uk"
+__author_email__ = "eric.kerfoot@kcl.ac.uk"
 __copyright__ = "Copyright (c) 2016-22 Eric Kerfoot, King's College London, all rights reserved. Licensed under the GPL (see LICENSE.txt)."
-

dicombrowser/dicom.py

@@ -21,6 +21,7 @@
 from concurrent.futures import ProcessPoolExecutor, as_completed
 from io import BytesIO
 from glob import glob
+from warnings import warn
 
 import numpy as np
 from pydicom import dicomio, datadict, errors
@@ -65,6 +66,30 @@
 FULL_NAME_MAP = {v: k for k, v in KEYWORD_NAME_MAP.items()}  # maps full names to keywords
 
 
+def get_2d_equivalent_image(img):
+    """Given an array `img` of some arbitrary dimensions, attempt to choose a valid 2D gray/RGB/RGBA image from it."""
+    ndim = img.ndim
+    shape = img.shape
+    color_dim = ndim > 2 and shape[-1] in (1, 3, 4)
+
+    if ndim <= 2 or (ndim == 3 and color_dim):  # 0D array, 1D array, 2D grayscale or 2D RGB(A)
+        if ndim < 2:
+            warn(f"Image has unusual shape {shape}, attempting to visualise")
+
+        return img
+    elif ndim == 3:  # 3D grayscale
+        warn(f"Image is volume with shape {shape}, using mid-slice")
+    elif ndim == 4 and color_dim:
+        warn(f"Image is RGB(A) volume with shape {shape}, using mid-slice")
+    else:
+        warn(f"Image is unknown volume with shape {shape}, using mid-slices")
+
+    # attempt to slice the volume in every dimension that's not height, width, or the channels
+    stop = 3 if color_dim else 2  # dimensions to not slice in, ie. (height,width) or (height,width,channels)
+    slices = [s // 2 for s in shape[:-stop]] + [slice(None)] * stop
+    return img[tuple(slices)]
+
+
 def get_scaled_image(dcm):
     """Return image data from `dcm` scaled using slope and intercept values."""
     try:

dicombrowser/dicombrowser.py

@@ -34,7 +34,7 @@
 
 from ._version import __version__
 from . import res
-from .dicom import load_dicom_dir, load_dicom_zip, SERIES_LIST_COLUMNS, ATTR_TREE_COLUMNS
+from .dicom import load_dicom_dir, load_dicom_zip, get_2d_equivalent_image, SERIES_LIST_COLUMNS, ATTR_TREE_COLUMNS
 from .models import AttrItemModel, SeriesTreeModel
 
 
@@ -49,6 +49,7 @@
 
 class LoadWorker(QtCore.QRunnable):
     """Loads Dicom data in a separate thread, updating the UI through the given signals."""
+
     def __init__(self, src, status_signal, update_signal):
         super().__init__()
         self.src = src
@@ -231,8 +232,8 @@ def set_series_image(self, i, auto_range=False):
 
             if img is None:  # if the image is None use the default "no image" object
                 img = self.noimg
-            # elif len(img.shape)==3: # multi-channel or multi-dimensional image, use average of dimensions
-            #    img=np.mean(img,axis=2)
+
+            img = get_2d_equivalent_image(img)  # get something renderable in 2D
 
             self.image_view.setImage(img.T, autoRange=auto_range, autoLevels=self.autoLevelsCheck.isChecked())
             self._fill_attr_view()

dicombrowser/models.py

@@ -99,6 +99,7 @@ def fill_attrs(self, dcm, columns, regex=None, maxValueSize=256):
 
 class SeriesTreeModel(QtGui.QStandardItemModel):
     """Represents the tree of Dicom series organised under nodes for each source file/directory."""
+
     def __init__(self, columns, data={}, parent=None):
         super().__init__(parent)
         self.columns = columns