ENH: Add unicode for checkboxes and framework for TotalSegmentator

aylward · Aug 5, 2024 · 7dd304c · 7dd304c
1 parent 2e8f8ec
commit 7dd304c
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Showing 23 changed files with 553 additions and 298 deletions.
diff --git a/src/minder3d/lib/sovImageTablePanelWidget.py b/src/minder3d/lib/sovImageTablePanelWidget.py
@@ -8,14 +8,12 @@
 from PySide6.QtWidgets import (
     QHeaderView,
     QInputDialog,
-    QStyle,
     QTableWidget,
     QTableWidgetItem,
     QWidget,
 )
 
 from .sovImageTableSettings import ImageTableSettings
-from .sovImportExportPanelWidget import ImportExportPanelWidget
 from .sovUtils import time_and_log
 from .ui_sovImageTablePanelWidget import Ui_ImageTablePanelWidget
 
@@ -40,8 +38,6 @@ def __init__(self, gui, state, parent=None):
         self.settings = ImageTableSettings()
 
         self.selected = []
-        pixmapi = getattr(QStyle, 'SP_DialogApplyButton')
-        self.selected_icon = self.style().standardIcon(pixmapi)
 
         self.imageTableWidget.setRowCount(0)
         self.imageTableWidget.setColumnCount(8)
@@ -93,24 +89,7 @@ def __init__(self, gui, state, parent=None):
 
     @time_and_log
     def add_import_export_panel(self):
-        """Add an image processing panel to the GUI if it does not already exist.
-
-        If the image processing panel does not exist, it creates a new ImageProcessPanelWidget and adds it to the tab widget.
-        If the image processing panel already exists, it sets the current widget to the existing panel.
-
-        Args:
-            self (object): The current instance of the class.
-        """
-        if self.gui.importExportPanel is None:
-            self.gui.importExportPanel = ImportExportPanelWidget(
-                self.gui, self.state
-            )
-        if self.gui.tabWidget.indexOf(self.gui.importExportPanel) == -1:
-            indx = self.gui.tabWidget.indexOf(self.gui.newTaskTab)
-            self.gui.tabWidget.insertTab(
-                indx, self.gui.importExportPanel, 'Import/Save/Export'
-            )
-            self.gui.tabWidget.setCurrentWidget(self.gui.importExportPanel)
+        self.gui.tabWidget.setCurrentWidget(self.gui.importExportTab)
 
     @time_and_log
     def unload_selected(self):
@@ -202,21 +181,21 @@ def redraw_image_row(self, row_num):
         col_num = 0
         if row_num in self.selected:
             self.imageTableWidget.setItem(
-                row_num, col_num, QTableWidgetItem(self.selected_icon, '')
+                row_num, col_num, QTableWidgetItem('\u25a3')
             )
         else:
             self.imageTableWidget.setItem(
-                row_num, col_num, QTableWidgetItem('')
+                row_num, col_num, QTableWidgetItem('\u25a1')
             )
         col_num += 1
         if img_num < len(self.state.image_filename):
             self.imageTableWidget.setItem(
-                row_num, col_num, QTableWidgetItem(self.selected_icon, '')
+                row_num, col_num, QTableWidgetItem('\u25a3')
             )
         else:
             print('ERROR: Can only redraw rows for images that are loaded.')
             self.imageTableWidget.setItem(
-                row_num, col_num, QTableWidgetItem('')
+                row_num, col_num, QTableWidgetItem('\u25a1')
             )
         col_num += 1
         self.imageTableWidget.setItem(
@@ -262,15 +241,15 @@ def redraw_scene_row(self, row_num):
         col_num = 0
         if row_num in self.selected:
             self.imageTableWidget.setItem(
-                row_num, col_num, QTableWidgetItem(self.selected_icon, '')
+                row_num, col_num, QTableWidgetItem('\u25a3')
             )
         else:
             self.imageTableWidget.setItem(
-                row_num, col_num, QTableWidgetItem('')
+                row_num, col_num, QTableWidgetItem('\u25a1')
             )
         col_num += 1
         self.imageTableWidget.setItem(
-            row_num, col_num, QTableWidgetItem(self.selected_icon, '')
+            row_num, col_num, QTableWidgetItem('\u25a3')
         )
         col_num += 1
         self.imageTableWidget.setItem(
@@ -350,11 +329,11 @@ def fill_table(self):
                     self.imageTableWidget.setItem(
                         row_num,
                         col_num,
-                        QTableWidgetItem(self.selected_icon, ''),
+                        QTableWidgetItem('\u25a3'),
                     )
                 else:
                     self.imageTableWidget.setItem(
-                        row_num, col_num, QTableWidgetItem('')
+                        row_num, col_num, QTableWidgetItem('\u25a1')
                     )
                 col_num += 1
                 loaded_text = ' '
@@ -402,11 +381,11 @@ def fill_table(self):
                     self.imageTableWidget.setItem(
                         row_num,
                         col_num,
-                        QTableWidgetItem(self.selected_icon, ''),
+                        QTableWidgetItem('\u25a3'),
                     )
                 else:
                     self.imageTableWidget.setItem(
-                        row_num, col_num, QTableWidgetItem('')
+                        row_num, col_num, QTableWidgetItem('\u25a1')
                     )
                 col_num += 1
                 loaded_text = ' '

diff --git a/src/minder3d/lib/sovImageTableSettings.py b/src/minder3d/lib/sovImageTableSettings.py
@@ -271,6 +271,7 @@ def get_thumbnail_pixmap_from_vtk_image(self, img):
         np_array = vtk_to_numpy(vtk_array)
         dims = img.GetDimensions()
         np_array = np_array.reshape(dims[1], dims[0], dims[2], -1)
+        np_array = np_array[::-1, :, :, :]
 
         # Process the NumPy array
         if np_array.shape[3] == 1:

diff --git a/src/minder3d/lib/sovImportDICOMPanelWidget.ui b/src/minder3d/lib/sovImportDICOMPanelWidget.ui
@@ -29,14 +29,11 @@
     <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;meta charset=&quot;utf-8&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
 p, li { white-space: pre-wrap; }
-hr { height: 1px; border-width: 0; }
-li.unchecked::marker { content: &quot;\2610&quot;; }
-li.checked::marker { content: &quot;\2612&quot;; }
-&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Segoe UI'; font-size:9pt; font-weight:400; font-style:normal;&quot;&gt;
-&lt;p style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-weight:700;&quot;&gt;Import DICOM&lt;/span&gt;&lt;/p&gt;
-&lt;p style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Select an input directory that contains the DICOM objects. That input directory and its subdirectories will be searched for DICOM objects that can be converted to images.&lt;/p&gt;
-&lt;p style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Select an output directory for storing the converted images. A hierarchy of subdirectories will be automatically created that correspond to the &amp;lt;PatientName&amp;gt;/&amp;lt;StudyID&amp;gt;-&amp;lt;StudyDescription&amp;gt;-&amp;lt;StudyDate&amp;gt;/&amp;lt;Modality&amp;gt;/&amp;lt;SeriesNumber&amp;gt;-&amp;lt;SeriesDescription&amp;gt;-&amp;lt;InstanceNumber&amp;gt;.dcm&lt;/p&gt;
-&lt;p style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;Optionally, the data can be automatically registered with Minder3D and made available for one-click loading via the image browser table.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;&quot;&gt;
+&lt;p style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-family:'Segoe UI'; font-weight:700;&quot;&gt;Import DICOM&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-family:'Segoe UI';&quot;&gt;Select an input directory that contains the DICOM objects. That input directory and its subdirectories will be searched for DICOM objects that can be converted to images.&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-family:'Segoe UI';&quot;&gt;Select an output directory for storing the converted images. A hierarchy of subdirectories will be automatically created that correspond to the &amp;lt;PatientName&amp;gt;/&amp;lt;StudyID&amp;gt;-&amp;lt;StudyDescription&amp;gt;-&amp;lt;StudyDate&amp;gt;/&amp;lt;Modality&amp;gt;/&amp;lt;SeriesNumber&amp;gt;-&amp;lt;SeriesDescription&amp;gt;-&amp;lt;InstanceNumber&amp;gt;.dcm&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-family:'Segoe UI';&quot;&gt;Optionally, the data can be automatically registered with Minder3D and made available for one-click loading via the image browser table.&lt;/span&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
    </property>
   </widget>
   <widget class="QLineEdit" name="importDICOMInputDirectoryLineEdit">
@@ -58,6 +55,11 @@ li.checked::marker { content: &quot;\2612&quot;; }
      <height>16</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Input Directory:</string>
    </property>
@@ -117,6 +119,11 @@ li.checked::marker { content: &quot;\2612&quot;; }
      <height>16</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Output Directory:</string>
    </property>
@@ -130,6 +137,11 @@ li.checked::marker { content: &quot;\2612&quot;; }
      <height>20</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Automatically register</string>
    </property>
@@ -143,6 +155,11 @@ li.checked::marker { content: &quot;\2612&quot;; }
      <height>24</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Run</string>
    </property>

diff --git a/src/minder3d/lib/sovImportExportPanelWidget.ui b/src/minder3d/lib/sovImportExportPanelWidget.ui
@@ -22,6 +22,11 @@
      <height>24</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Load Image</string>
    </property>
@@ -35,6 +40,11 @@
      <height>24</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Import DICOM Data</string>
    </property>
@@ -48,6 +58,11 @@
      <height>24</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Save Image</string>
    </property>
@@ -61,6 +76,11 @@
      <height>24</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Save Scene</string>
    </property>
@@ -74,6 +94,11 @@
      <height>24</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Load Scene</string>
    </property>
@@ -87,6 +112,11 @@
      <height>24</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Save Overlay</string>
    </property>
@@ -100,6 +130,11 @@
      <height>24</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Save VTK Models</string>
    </property>
@@ -113,6 +148,11 @@
      <height>24</height>
     </rect>
    </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
    <property name="text">
     <string>Load Overlay</string>
    </property>

diff --git a/src/minder3d/lib/sovLungCTALogic.py → src/minder3d/lib/sovIndexedOrgansLogic.py b/src/minder3d/lib/sovLungCTALogic.py → src/minder3d/lib/sovIndexedOrgansLogic.py
@@ -9,7 +9,7 @@
 from .sovUtils import time_and_log
 
 
-class LungCTALogic:
+class IndexedOrgansLogic:
     def __init__(self):
         self.ai_first_run = True
         self.image = None
@@ -116,9 +116,7 @@ def run(self):
         nifti_nib = nib.Nifti1Image(
             np.transpose(pre_array, (2, 1, 0)).copy(), mat
         )
-        seg_nib = totalsegmentator(
-            input=nifti_nib, output=None, task='lung_vessels'
-        )
+        seg_nib = totalsegmentator(input=nifti_nib, output=None, task='total')
 
         seg_array = seg_nib.get_fdata().astype(np.uint8)
         seg_image = itk.GetImageFromArray(

diff --git a/src/minder3d/lib/sovLungCTAPanelWidget.py → ...nder3d/lib/sovIndexedOrgansPanelWidget.py b/src/minder3d/lib/sovLungCTAPanelWidget.py → ...nder3d/lib/sovIndexedOrgansPanelWidget.py
@@ -1,13 +1,13 @@
 from PySide6.QtWidgets import QMessageBox, QWidget
 
-from .sovLungCTALogic import LungCTALogic
+from .sovIndexedOrgansLogic import IndexedOrgansLogic
 from .sovUtils import add_objects_in_mask_image_to_scene, time_and_log
-from .ui_sovLungCTAPanelWidget import Ui_LungCTAPanelWidget
+from .ui_sovIndexedOrgansPanelWidget import Ui_IndexedOrgansPanelWidget
 
 
-class LungCTAPanelWidget(QWidget, Ui_LungCTAPanelWidget):
+class IndexedOrgansPanelWidget(QWidget, Ui_IndexedOrgansPanelWidget):
     def __init__(self, gui, state, parent=None):
-        """Initialize the LungCTA application.
+        """Initialize the IndexedOrgans application.
 
         Args:
             gui: The graphical user interface object.
@@ -20,12 +20,12 @@ def __init__(self, gui, state, parent=None):
 
         self.gui = gui
         self.state = state
-        self.logic = LungCTALogic()
+        self.logic = IndexedOrgansLogic()
 
         self.ai_first_run = True
 
-        self.lungStep1Button.clicked.connect(self.segment_ai)
-        self.lungStep1Button.setStyleSheet('background-color: #00aa00')
+        self.indexedOrgansStep1Button.clicked.connect(self.segment_ai)
+        self.indexedOrgansStep1Button.setStyleSheet('background-color: #00aa00')
 
     @time_and_log
     def segment_ai(self):

diff --git a/src/minder3d/lib/sovIndexedOrgansPanelWidget.ui b/src/minder3d/lib/sovIndexedOrgansPanelWidget.ui
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>IndexedOrgansPanelWidget</class>
+ <widget class="QWidget" name="IndexedOrgansPanelWidget">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>390</width>
+    <height>125</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Form</string>
+  </property>
+  <widget class="QPushButton" name="indexedOrgansStep1Button">
+   <property name="geometry">
+    <rect>
+     <x>10</x>
+     <y>30</y>
+     <width>261</width>
+     <height>24</height>
+    </rect>
+   </property>
+   <property name="font">
+    <font>
+     <pointsize>7</pointsize>
+    </font>
+   </property>
+   <property name="text">
+    <string>Run Total Segmentator</string>
+   </property>
+  </widget>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>