Merge branch 'T26896-TractSeg'

MIC-DKFZ · Dec 6, 2019 · 5b33778 · 5b33778
2 parents 3ff5d37 + 5342894
commit 5b33778
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Showing 5 changed files with 26 additions and 25 deletions.
diff --git a/...rg.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationViewControls.ui b/...rg.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationViewControls.ui
@@ -61,7 +61,7 @@
    <item row="0" column="0" rowspan="3">
     <widget class="QToolBox" name="toolBox">
      <property name="currentIndex">
-      <number>0</number>
+      <number>1</number>
      </property>
      <widget class="QWidget" name="page">
       <property name="geometry">
@@ -1034,7 +1034,7 @@
           <item row="0" column="1">
            <widget class="QSpinBox" name="m_MaxTwistBox">
             <property name="toolTip">
-             <string>Specify number of fibers to generate for the selected bundle.</string>
+             <string>Max. fiber twist per step (in degree)</string>
             </property>
             <property name="minimum">
              <number>0</number>
@@ -1053,7 +1053,7 @@
           <item row="0" column="0">
            <widget class="QSpinBox" name="m_MinTwistBox">
             <property name="toolTip">
-             <string>Specify number of fibers to generate for the selected bundle.</string>
+             <string>Min. fiber twist per step (in degree)</string>
             </property>
             <property name="minimum">
              <number>0</number>
@@ -1115,7 +1115,7 @@
           <item row="0" column="0">
            <widget class="QSpinBox" name="m_StepSizeMinBox">
             <property name="toolTip">
-             <string>Specify number of fibers to generate for the selected bundle.</string>
+             <string>Min. distance between fiducials (in mm)</string>
             </property>
             <property name="minimum">
              <number>1</number>
@@ -1134,7 +1134,7 @@
           <item row="0" column="1">
            <widget class="QSpinBox" name="m_StepSizeMaxBox">
             <property name="toolTip">
-             <string>Specify number of fibers to generate for the selected bundle.</string>
+             <string>Max. distance between fiducials (in mm)</string>
             </property>
             <property name="minimum">
              <number>1</number>
@@ -1175,7 +1175,7 @@
        <item row="1" column="1">
         <widget class="QSpinBox" name="m_NumBundlesBox">
          <property name="toolTip">
-          <string>Specify number of fibers to generate for the selected bundle.</string>
+          <string>Number of generated bundles</string>
          </property>
          <property name="minimum">
           <number>1</number>
@@ -1234,7 +1234,7 @@
           <item row="0" column="0">
            <widget class="QSpinBox" name="m_CurvyMinBox">
             <property name="toolTip">
-             <string>Specify number of fibers to generate for the selected bundle.</string>
+             <string>Min. rotation between steps (in degree)</string>
             </property>
             <property name="minimum">
              <number>1</number>
@@ -1253,7 +1253,7 @@
           <item row="0" column="1">
            <widget class="QSpinBox" name="m_CurvyMaxBox">
             <property name="toolTip">
-             <string>Specify number of fibers to generate for the selected bundle.</string>
+             <string>Max. rotation between steps (in degree)</string>
             </property>
             <property name="minimum">
              <number>1</number>
@@ -1415,7 +1415,7 @@
           <item row="0" column="0">
            <widget class="QSpinBox" name="m_SizeMinBox">
             <property name="toolTip">
-             <string>Specify number of fibers to generate for the selected bundle.</string>
+             <string>Bundle radius</string>
             </property>
             <property name="minimum">
              <number>1</number>
@@ -1434,7 +1434,7 @@
           <item row="0" column="1">
            <widget class="QSpinBox" name="m_SizeMaxBox">
             <property name="toolTip">
-             <string>Specify number of fibers to generate for the selected bundle.</string>
+             <string>Bundle radius</string>
             </property>
             <property name="minimum">
              <number>1</number>
@@ -1477,7 +1477,7 @@
           <item row="0" column="1">
            <widget class="QSpinBox" name="m_MaxDensityBox">
             <property name="toolTip">
-             <string>Specify number of fibers to generate for the selected bundle.</string>
+             <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Max. fibers per cm&lt;span style=&quot; vertical-align:super;&quot;&gt;2&lt;/span&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
             </property>
             <property name="minimum">
              <number>1</number>
@@ -1496,7 +1496,7 @@
           <item row="0" column="0">
            <widget class="QSpinBox" name="m_MinDensityBox">
             <property name="toolTip">
-             <string>Specify number of fibers to generate for the selected bundle.</string>
+             <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Min. fibers per cm&lt;span style=&quot; vertical-align:super;&quot;&gt;2&lt;/span&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
             </property>
             <property name="minimum">
              <number>1</number>

diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tractseg.py b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tractseg.py
@@ -8,11 +8,10 @@
 
     data = sitk.GetArrayFromImage(in_image)
     data = np.nan_to_num(data)
+
     swapaxes = False
-    if data.shape != (sx, sy, sz):
-        print("Swapping axes!")
-        data = np.swapaxes(data, 0, 2)
-        swapaxes = True
+    data = np.swapaxes(data, 0, 2)
+    swapaxes = True
 
     affine = np.zeros((4, 4))
     affine[0, 0] = in_image.GetDirection()[0] * in_image.GetSpacing()[0]
@@ -39,13 +38,11 @@
     print('threshold', threshold)
 
     seg = run_tractseg(data=data, output_type=output_type, input_type="peaks", verbose=verbose, get_probs=get_probs,
-                       dropout_sampling=dropout_sampling, threshold=threshold, postprocess=False)
+                       dropout_sampling=dropout_sampling, threshold=threshold, postprocess=False, nr_cpus=1)
 
-    # bla = nib.Nifti1Image(seg, affine)
-    # nib.save(bla, '/home/neher/test.nii.gz')
-    if swapaxes:
-        print("Swapping axes back!")
-        seg = np.swapaxes(seg, 0, 2)
+#    bla = nib.Nifti1Image(seg, affine)
+#    nib.save(bla, '/home/neher/test.nii.gz')
+    seg = np.swapaxes(seg, 0, 2)
 
     print('Output shape: ' + str(seg.shape))
     if output_type == "tract_segmentation":

diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.cpp
@@ -113,7 +113,7 @@ void QmitkTractSegView::Start()
 
   // get python script as string
   QString data;
-  QString fileName(":/QmitkDiffusionImaging/tractseg.py");
+  QString fileName(":/QmitkDiffusionPython/tractseg.py");
   QFile file(fileName);
   if(!file.open(QIODevice::ReadOnly)) {
     qDebug()<<"filenot opened"<<endl;
@@ -125,6 +125,9 @@ void QmitkTractSegView::Start()
   }
   file.close();
 
+  if (data.size()==0)
+    mitkThrow() << fileName << " could not be read!";
+
   us::ModuleContext* context = us::GetModuleContext();
   us::ServiceReference<mitk::IPythonService> m_PythonServiceRef = context->GetServiceReference<mitk::IPythonService>();
   mitk::IPythonService* m_PythonService = dynamic_cast<mitk::IPythonService*> ( context->GetService<mitk::IPythonService>(m_PythonServiceRef) );
@@ -198,6 +201,7 @@ void QmitkTractSegView::Start()
   // check for errors
   if(!m_PythonService->GetVariable("error_string").empty())
   {
+    mitk::IPythonService::ForceLoadModule();
     QMessageBox::warning(nullptr, "Error", QString(m_PythonService->GetVariable("error_string").c_str()), QMessageBox::Ok);
     return;
   }

diff --git a/PythonRequirements.txt b/PythonRequirements.txt
@@ -3,7 +3,7 @@ SimpleITK
 dipy
 sklearn
 https://github.com/MIC-DKFZ/batchgenerators/archive/v0.19.5.zip
-https://github.com/MIC-DKFZ/TractSeg/archive/v2.1.1.zip
+https://github.com/MIC-DKFZ/TractSeg/archive/master.zip
 https://github.com/MIC-DKFZ/HD-BET/archive/master.zip
 torch
 torchvision
diff --git a/README.md b/README.md
@@ -180,7 +180,7 @@ Automatically generated random fiber configuration for Fiberfox simulations.
 
 
 ## Building MITK Diffusion from source
-* Install [Qt](https://www.qt.io/ Qt) on your system (>= 5.11.1).
+* Install [Qt](https://www.qt.io/) on your system (>= 5.12.6).
 * Clone MITK from [github](https://github.com/MIC-DKFZ/MITK-Diffusion.git) using [Git version control](https://git-scm.com/).
 * Clone MITK Diffusion from [github](https://github.com/MITK/MITK.git).
 * Configure the MITK Superbuild using [CMake](https://cmake.org/) (>= 3.14.5).