mosamatic2 2.0.11__tar.gz → 2.0.12__tar.gz

{mosamatic2-2.0.11 → mosamatic2-2.0.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.11
+Version: 2.0.12
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl

{mosamatic2-2.0.11 → mosamatic2-2.0.12}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mosamatic2"
-version = "2.0.11"
+version = "2.0.12"
 description = ""
 authors = [
     {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}

{mosamatic2-2.0.11 → mosamatic2-2.0.12}/src/mosamatic2/commands/dicom2nifti.py

@@ -3,12 +3,12 @@ import click
 from mosamatic2.core.tasks import Dicom2NiftiTask
 
 
-@click.command(help='Converts DICOM series to NIFTI')
+@click.command(help='Converts root directory with DICOM series to NIFTI format')
 @click.option(
-    '--images', 
+    '--scans', 
     required=True, 
     type=click.Path(exists=True), 
-    help='Directory with images',
+    help='Root directory with DICOM scans (one for each patient)',
 )
 @click.option(
     '--output', 
@@ -22,14 +22,14 @@ from mosamatic2.core.tasks import Dicom2NiftiTask
     default=False, 
     help='Overwrite [true|false]'
 )
-def dicom2nifti(images, output, overwrite):
+def dicom2nifti(scans, output, overwrite):
     """
-    Converts single DICOM series (scan) to NIFTI
+    Converts DICOM scans to NIFTI format.
     
     Parameters
     ----------
-    --images : str
-        Directory with DICOM images of a single series
+    --scans : str
+        Root directory with DICOM scans (one subdirectory for each patient)
 
     --output : str
         Path to output directory
@@ -38,7 +38,7 @@ def dicom2nifti(images, output, overwrite):
         Overwrite contents output directory [true|false]
     """
     task = Dicom2NiftiTask(
-        inputs={'images': images},
+        inputs={'scans': scans},
         params=None,
         output=output,
         overwrite=overwrite,

mosamatic2-2.0.12/src/mosamatic2/core/data/multiniftiimage.py

@@ -0,0 +1,26 @@
+import os
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.data.filedata import FileData
+from mosamatic2.core.data.niftiimage import NiftiImage
+
+LOG = LogManager()
+
+
+class MultiNiftiImage(FileData):
+    def __init__(self):
+        super(MultiNiftiImage, self).__init__()
+        self._images = []
+
+    def images(self):
+        return self._images
+    
+    def load(self):
+        if self.path():
+            for f in os.listdir(self.path()):
+                f_path = os.path.join(self.path(), f)
+                image = NiftiImage()
+                image.set_path(f_path)
+                if image.load():
+                    self._images.append(image)
+            return True
+        return False

{mosamatic2-2.0.11 → mosamatic2-2.0.12}/src/mosamatic2/core/data/multinumpyimage.py

@@ -1,14 +1,14 @@
 import os
 from mosamatic2.core.managers.logmanager import LogManager
 from mosamatic2.core.data.filedata import FileData
-from mosamatic2.core.data.numpyimage import NumPyImage
+from mosamatic2.core.data.numpyimage import NumpyImage
 
 LOG = LogManager()
 
 
-class MultiNumPyImage(FileData):
+class MultiNumpyImage(FileData):
     def __init__(self):
-        super(MultiNumPyImage, self).__init__()
+        super(MultiNumpyImage, self).__init__()
         self._images = []
 
     def images(self):
@@ -18,7 +18,7 @@ class MultiNumPyImage(FileData):
         if self.path():
             for f in os.listdir(self.path()):
                 f_path = os.path.join(self.path(), f)
-                image = NumPyImage()
+                image = NumpyImage()
                 image.set_path(f_path)
                 if image.load():
                     self._images.append(image)

mosamatic2-2.0.12/src/mosamatic2/core/data/niftiimage.py

@@ -0,0 +1,13 @@
+from mosamatic2.core.data.filedata import FileData
+from mosamatic2.core.utils import (
+    is_nifti,
+    load_nifti,
+)
+
+class NiftiImage(FileData):
+    def load(self):
+        if self.path():
+            if is_nifti(self.path()):
+                self.set_object(load_nifti(self.path()))
+                return True
+        return False

{mosamatic2-2.0.11 → mosamatic2-2.0.12}/src/mosamatic2/core/data/numpyimage.py

@@ -4,7 +4,7 @@ from mosamatic2.core.utils import (
     load_numpy_array,
 )
 
-class NumPyImage(FileData):
+class NumpyImage(FileData):
     def load(self):
         if self.path():
             if is_numpy(self.path()):

{mosamatic2-2.0.11 → mosamatic2-2.0.12}/src/mosamatic2/core/tasks/calculatescorestask/calculatescorestask.py

@@ -4,7 +4,7 @@ import pandas as pd
 from mosamatic2.core.tasks.task import Task
 from mosamatic2.core.managers.logmanager import LogManager
 from mosamatic2.core.data.multidicomimage import MultiDicomImage
-from mosamatic2.core.data.numpyimage import NumPyImage
+from mosamatic2.core.data.numpyimage import NumpyImage
 from mosamatic2.core.utils import (
     get_pixels_from_dicom_object,
     calculate_area,
@@ -74,7 +74,7 @@ class CalculateScoresTask(Task):
 
     def load_segmentation(self, f, file_type='npy'):
         if file_type == 'npy':
-            segmentation = NumPyImage()
+            segmentation = NumpyImage()
             segmentation.set_path(f)
             if segmentation.load():
                 return segmentation.object()

mosamatic2-2.0.12/src/mosamatic2/core/tasks/dicom2niftitask/dicom2niftitask.py

@@ -0,0 +1,38 @@
+import os
+import dicom2nifti
+from mosamatic2.core.tasks.task import Task
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.utils import is_dicom
+
+LOG = LogManager()
+
+
+class Dicom2NiftiTask(Task):
+    INPUTS = ['scans']
+    PARAMS = []
+
+    def __init__(self, inputs, params, output, overwrite):
+        super(Dicom2NiftiTask, self).__init__(inputs, params, output, overwrite)
+
+    def load_scan_dirs(self):
+        scan_dirs = []
+        for d in os.listdir(self.input('scans')):
+            scan_dir = os.path.join(self.input('scans'), d)
+            if os.path.isdir(scan_dir):
+                scan_dirs.append(scan_dir)
+        return scan_dirs
+
+    def run(self):
+        scan_dirs = self.load_scan_dirs()
+        nr_steps = len(scan_dirs)
+        for step in range(nr_steps):
+            scan_dir = scan_dirs[step]
+            scan_name = os.path.split(scan_dir)[1]
+            nifti_file_name = scan_name + '.nii.gz'
+            LOG.info(f'Converting DICOM series in {scan_dir} to {nifti_file_name}')
+            dicom2nifti.dicom_series_to_nifti(
+                scan_dir,
+                os.path.join(self.output(), nifti_file_name),
+                reorient_nifti=True,
+            )
+            self.set_progress(step, nr_steps)

{mosamatic2-2.0.11 → mosamatic2-2.0.12}/src/mosamatic2/core/tasks/segmentmusclefatl3tensorflowtask/segmentmusclefatl3tensorflowtask.py

@@ -9,6 +9,7 @@ from mosamatic2.core.tasks.task import Task
 from mosamatic2.core.tasks.segmentmusclefatl3tensorflowtask.paramloader import ParamLoader
 from mosamatic2.core.data.multidicomimage import MultiDicomImage
 from mosamatic2.core.data.dicomimage import DicomImage
+from mosamatic2.core.managers.logmanager import LogManager
 from mosamatic2.core.utils import (
     normalize_between,
     get_pixels_from_dicom_object,
@@ -16,6 +17,8 @@ from mosamatic2.core.utils import (
 )
 
 DEVICE = 'cpu'
+L3_INDEX = 167
+LOG = LogManager()
 
 
 class SegmentMuscleFatL3TensorFlowTask(Task):

{mosamatic2-2.0.11 → mosamatic2-2.0.12}/src/mosamatic2/core/tasks/selectslicefromscanstask/selectslicefromscanstask.py

@@ -30,7 +30,7 @@ class SelectSliceFromScansTask(Task):
         os.makedirs(self._error_dir, exist_ok=True)
         self._error_file = os.path.join(self._error_dir, 'errors.txt')
         with open(self._error_file, 'w') as f:
-            f.write('Errors:\n')
+            f.write('Errors:\n\n')
         LOG.info(f'Error directory: {self._error_dir}')
 
     def write_error(self, message):

{mosamatic2-2.0.11 → mosamatic2-2.0.12}/src/mosamatic2/core/utils.py

@@ -5,6 +5,7 @@ import textwrap
 import math
 import pendulum
 import numpy as np
+import nibabel as nb
 import struct
 import binascii
 import pydicom
@@ -134,6 +135,16 @@ def is_jpeg2000_compressed(p):
     return False
 
 
+def is_nifti(f):
+    return f.endswith('.nii') or f.endswith('.nii.gz')
+
+
+def load_nifti(f):
+    if is_nifti(f):
+        return nb.load(f)
+    return None
+
+
 def is_numpy_array(value):
     return isinstance(value, np.array)
 
@@ -149,8 +160,7 @@ def is_numpy(f):
 def load_numpy_array(f):
     if is_numpy(f):
         return np.load(f)
-    else:
-        return None
+    return None
 
 
 def get_pixels_from_tag_file(tag_file_path):

mosamatic2-2.0.12/src/mosamatic2/ui/resources/VERSION

@@ -0,0 +1 @@
+2.0.12 

{mosamatic2-2.0.11 → mosamatic2-2.0.12}/src/mosamatic2/ui/widgets/panels/tasks/dicom2niftitaskpanel.py

@@ -33,8 +33,8 @@ class Dicom2NiftiTaskPanel(TaskPanel):
     def __init__(self):
         super(Dicom2NiftiTaskPanel, self).__init__()
         self.set_title(PANEL_TITLE)
-        self._images_dir_line_edit = None
-        self._images_dir_select_button = None
+        self._scans_dir_line_edit = None
+        self._scans_dir_select_button = None
         self._output_dir_line_edit = None
         self._output_dir_select_button = None
         self._overwrite_checkbox = None
@@ -46,16 +46,16 @@ class Dicom2NiftiTaskPanel(TaskPanel):
         self._thread = None
         self.init_layout()
 
-    def images_dir_line_edit(self):
-        if not self._images_dir_line_edit:
-            self._images_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/images_dir'))
-        return self._images_dir_line_edit
+    def scans_dir_line_edit(self):
+        if not self._scans_dir_line_edit:
+            self._scans_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/scans_dir'))
+        return self._scans_dir_line_edit
     
-    def images_dir_select_button(self):
-        if not self._images_dir_select_button:
-            self._images_dir_select_button = QPushButton('Select')
-            self._images_dir_select_button.clicked.connect(self.handle_images_dir_select_button)
-        return self._images_dir_select_button
+    def scans_dir_select_button(self):
+        if not self._scans_dir_select_button:
+            self._scans_dir_select_button = QPushButton('Select')
+            self._scans_dir_select_button.clicked.connect(self.handle_scans_dir_select_button)
+        return self._scans_dir_select_button
     
     def output_dir_line_edit(self):
         if not self._output_dir_line_edit:
@@ -93,13 +93,13 @@ class Dicom2NiftiTaskPanel(TaskPanel):
         return self._settings
     
     def init_layout(self):
-        images_dir_layout = QHBoxLayout()
-        images_dir_layout.addWidget(self.images_dir_line_edit())
-        images_dir_layout.addWidget(self.images_dir_select_button())
+        scans_dir_layout = QHBoxLayout()
+        scans_dir_layout.addWidget(self.scans_dir_line_edit())
+        scans_dir_layout.addWidget(self.scans_dir_select_button())
         output_dir_layout = QHBoxLayout()
         output_dir_layout.addWidget(self.output_dir_line_edit())
         output_dir_layout.addWidget(self.output_dir_select_button())
-        self.form_layout().addRow('Images directory', images_dir_layout)
+        self.form_layout().addRow('Scans directory', scans_dir_layout)
         self.form_layout().addRow('Output directory', output_dir_layout)
         self.form_layout().addRow('Overwrite', self.overwrite_checkbox())
         layout = QVBoxLayout()
@@ -108,11 +108,11 @@ class Dicom2NiftiTaskPanel(TaskPanel):
         self.setLayout(layout)
         self.setObjectName(PANEL_NAME)
 
-    def handle_images_dir_select_button(self):
+    def handle_scans_dir_select_button(self):
         last_directory = self.settings().get('last_directory')
         directory = QFileDialog.getExistingDirectory(dir=last_directory)
         if directory:
-            self.images_dir_line_edit().setText(directory)
+            self.scans_dir_line_edit().setText(directory)
             self.settings().set('last_directory', directory)
 
     def handle_output_dir_select_button(self):
@@ -134,7 +134,7 @@ class Dicom2NiftiTaskPanel(TaskPanel):
             self.run_task_button().setEnabled(False)
             self.save_inputs_and_parameters()
             self._task = Dicom2NiftiTask(
-                inputs={'images': self.images_dir_line_edit().text()},
+                inputs={'scans': self.scans_dir_line_edit().text()},
                 params=None,
                 output=self.output_dir_line_edit().text(),
                 overwrite=self.overwrite_checkbox().isChecked(),
@@ -167,10 +167,10 @@ class Dicom2NiftiTaskPanel(TaskPanel):
 
     def check_inputs_and_parameters(self):
         errors = []
-        if self.images_dir_line_edit().text() == '':
-            errors.append('Empty images directory path')
-        if not os.path.isdir(self.images_dir_line_edit().text()):
-            errors.append('Images directory does not exist')
+        if self.scans_dir_line_edit().text() == '':
+            errors.append('Empty scans directory path')
+        if not os.path.isdir(self.scans_dir_line_edit().text()):
+            errors.append('Scans directory does not exist')
         if self.output_dir_line_edit().text() == '':
             errors.append('Empty output directory path')
         if os.path.isdir(self.output_dir_line_edit().text()) and not self.overwrite_checkbox().isChecked():
@@ -178,6 +178,6 @@ class Dicom2NiftiTaskPanel(TaskPanel):
         return errors
     
     def save_inputs_and_parameters(self):
-        self.settings().set(f'{PANEL_NAME}/images_dir', self.images_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/scans_dir', self.scans_dir_line_edit().text())
         self.settings().set(f'{PANEL_NAME}/output_dir', self.output_dir_line_edit().text())
         self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())

mosamatic2-2.0.11/src/mosamatic2/core/tasks/dicom2niftitask/dicom2niftitask.py

@@ -1,24 +0,0 @@
-import os
-import dicom2nifti
-from mosamatic2.core.tasks.task import Task
-from mosamatic2.core.managers.logmanager import LogManager
-
-LOG = LogManager()
-
-
-class Dicom2NiftiTask(Task):
-    INPUTS = ['images']
-    PARAMS = []
-
-    def __init__(self, inputs, params, output, overwrite):
-        super(Dicom2NiftiTask, self).__init__(inputs, params, output, overwrite)
-
-    def run(self):
-        nifti_file_name = os.path.split(self.input('images'))[1] + '.nii.gz'
-        LOG.info(f'Converting DICOM directory to {nifti_file_name}')
-        dicom2nifti.dicom_series_to_nifti(
-            self.input('images'),
-            os.path.join(self.output(), nifti_file_name),
-            reorient_nifti=True,
-        )
-        self.set_progress(0, 1)

mosamatic2-2.0.11/src/mosamatic2/ui/resources/VERSION

@@ -1 +0,0 @@
-2.0.11