ENH: Working SRR pipeline and clean interfaces

Medical-Image-Analysis-Laboratory · May 29, 2020 · c4fbabf · c4fbabf
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diff --git a/data/code/sub-01_ses-01_scans.txt b/data/code/sub-01_ses-01_scans.txt
@@ -1,3 +1,6 @@
 run-1 axial
-run-2 coronal
-run-3 sagittal
+run-3 coronal
+run-5 sagittal
+run-2 axial
+run-4 coronal
+run-6 sagittal
diff --git a/notebooks/srr.ipynb b/notebooks/srr.ipynb
diff --git a/pymialsrtk/interfaces/postprocess.py b/pymialsrtk/interfaces/postprocess.py
@@ -0,0 +1,171 @@
+# Copyright © 2016-2019 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland
+#
+#  This software is distributed under the open-source license Modified BSD.
+
+""" PyMIALSRTK preprocessing functions
+"""
+
+import os
+
+from glob import glob
+
+from traits.api import *
+
+import nibabel as nib
+
+from nipype.utils.filemanip import split_filename
+from nipype.interfaces.base import traits, isdefined, CommandLine, CommandLineInputSpec,\
+    TraitedSpec, File, InputMultiPath, OutputMultiPath, BaseInterface, BaseInterfaceInputSpec
+
+from pymialsrtk.interfaces.utils import run
+
+
+
+
+
+#
+##  Refinement HR mask
+# 
+
+
+class MialsrtkRefineHRMaskByIntersectionInputSpec(BaseInterfaceInputSpec):
+    bids_dir = Directory(desc='BIDS root directory',mandatory=True,exists=True)
+    input_images = InputMultiPath(File(desc='files to be SR', mandatory = True))
+    input_masks = InputMultiPath(File(desc='mask of files to be SR', mandatory = True))
+    input_transforms = InputMultiPath(File(desc='', mandatory = True))
+    input_sr = File(mandatory=True)
+
+    input_rad_dilatation = traits.Int(1, usedefault=True) 
+    in_use_staple = traits.Bool(True, usedefault=True)
+
+    deblurring = traits.Bool(False, usedefault=True)
+    out_LRmask_postfix = traits.Str("_LRmask", usedefault=True)
+    out_srmask_postfix = traits.Str("_srMask", usedefault=True)
+
+    stacksOrder = traits.List(mandatory = False)
+
+class MialsrtkRefineHRMaskByIntersectionOutputSpec(TraitedSpec):
+    output_SRmask = File()
+    output_LRmasks = OutputMultiPath(File())
+
+class MialsrtkRefineHRMaskByIntersection(BaseInterface):
+    input_spec = MialsrtkRefineHRMaskByIntersectionInputSpec
+    output_spec = MialsrtkRefineHRMaskByIntersectionOutputSpec
+
+    def _run_interface(self, runtime):
+
+        cmd = ['mialsrtkRefineHRMaskByIntersection']
+
+        cmd += ['--radius-dilation', str(self.inputs.input_rad_dilatation)]
+
+        if self.inputs.in_use_staple:
+            cmd += ['--use-staple']             
+
+        run_nb_images  = []
+        for in_file in self.inputs.input_images:
+            cut_avt = in_file.split('run-')[1]
+            cut_apr = cut_avt.split('_')[0]
+            run_nb_images.append(int(cut_apr))
+
+        run_nb_masks  = []
+        for in_mask in self.inputs.input_masks:
+            cut_avt = in_mask.split('run-')[1]
+            cut_apr = cut_avt.split('_')[0]
+            run_nb_masks.append(int(cut_apr))
+
+        run_nb_transforms  = []
+        for in_mask in self.inputs.input_transforms:
+            cut_avt = in_mask.split('run-')[1]
+            cut_apr = cut_avt.split('_')[0]
+            run_nb_transforms.append(int(cut_apr))
+
+
+
+        for order in self.inputs.stacksOrder:
+            index_img = run_nb_images.index(order)
+            index_mask = run_nb_masks.index(order)
+            index_tranform = run_nb_transforms.index(order)
+
+            cmd += ['-i', self.inputs.input_images[index_img]]
+            cmd += ['-m', self.inputs.input_masks[index_mask]]
+            cmd += ['-t', self.inputs.input_transforms[index_tranform]]
+
+
+            _, name, ext = split_filename(self.inputs.input_images[index_img])
+            out_file = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_LRmask_postfix, ext)))
+            cmd += ['-O', out_file]
+
+        _, name, ext = split_filename(os.path.abspath(self.inputs.input_images[0]))
+        out_file = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_srmask_postfix, ext)))
+
+        cmd += ['-r', self.inputs.input_sr]
+        cmd += ['-o', out_file]
+
+
+
+
+        try:
+            print('... cmd: {}'.format(cmd))
+            cmd = ' '.join(cmd)
+            run(self, cmd, env={}, cwd=os.path.abspath(self.inputs.bids_dir))
+        except:
+            print('Failed')
+
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        _, name, ext = split_filename(os.path.abspath(self.inputs.input_images[0]))
+        outputs['output_SRmask'] = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_srmask_postfix, ext)))
+        outputs['output_LRmasks'] = glob(os.path.abspath(''.join(["*", self.inputs.out_LRmask_postfix, ext])))
+        return outputs
+
+
+
+
+
+# 
+## N4 Bias field correction
+# 
+
+
+class MialsrtkN4BiasFieldCorrectionInputSpec(BaseInterfaceInputSpec):
+    bids_dir = Directory(desc='BIDS root directory',mandatory=True,exists=True)
+    input_image = File(desc='files to be HistNorm', mandatory = True)
+    input_mask = File(desc='mask of files to be HistNorm', mandatory = False)
+
+    out_im_postfix = traits.Str("_gbcorr", usedefault=True)
+    out_fld_postfix = traits.Str("_gbcorrfield", usedefault=True)
+
+
+class MialsrtkN4BiasFieldCorrectionOutputSpec(TraitedSpec):
+    output_image = File()
+    output_field = File()
+
+class MialsrtkN4BiasFieldCorrection(BaseInterface):
+    input_spec = MialsrtkN4BiasFieldCorrectionInputSpec
+    output_spec = MialsrtkN4BiasFieldCorrectionOutputSpec
+
+    def _run_interface(self, runtime):
+        _, name, ext = split_filename(os.path.abspath(self.inputs.input_image))
+        out_corr = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_im_postfix, ext)))
+        out_fld = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_fld_postfix, ext)))
+
+        cmd = ['mialsrtkN4BiasFieldCorrection', self.inputs.input_image, self.inputs.input_mask, out_corr, out_fld]
+
+        try:
+            print('... cmd: {}'.format(cmd))
+            cmd = ' '.join(cmd)
+            run(self, cmd, env={}, cwd=os.path.abspath(self.inputs.bids_dir))
+        except:
+            print('Failed')
+
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        _, name, ext = split_filename(os.path.abspath(self.inputs.input_image))
+        outputs['output_image'] = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_im_postfix, ext)))
+        outputs['output_field'] = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_fld_postfix, ext)))
+
+        return outputs
diff --git a/pymialsrtk/interfaces/preprocess.py b/pymialsrtk/interfaces/preprocess.py
@@ -32,7 +32,7 @@ class BtkNLMDenoisingInputSpec(BaseInterfaceInputSpec):
     in_file = File(desc='Input image',mandatory=True)
     in_mask = File(desc='Input mask',mandatory=False)
     out_postfix = traits.Str("_nlm", usedefault=True)
-    weight = traits.Float(0.1,desc='NLM weight (0.1 by default)')
+    weight = traits.Float(0.1,desc='NLM weight (0.1 by default)', usedefault=True)
 
 class BtkNLMDenoisingOutputSpec(TraitedSpec):
     out_file = File(desc='Denoised image')
@@ -71,7 +71,7 @@ class MultipleBtkNLMDenoisingInputSpec(BaseInterfaceInputSpec):
     bids_dir = Directory(desc='BIDS root directory',mandatory=True,exists=True)
     input_images = InputMultiPath(File(desc='files to be denoised', mandatory = True))
     input_masks = InputMultiPath(File(desc='mask of files to be denoised', mandatory = False))
-    weight = traits.Float(0.1)
+    weight = traits.Float(0.1,desc='NLM weight (0.1 by default)', usedefault=True)
     out_postfix = traits.Str("_nlm", usedefault=True)
     stacksOrder = traits.List(mandatory=False)
 
@@ -304,6 +304,7 @@ def _list_outputs(self):
         return outputs
 
 
+
 # 
 ## slice by slice correct bias field 
 # 
@@ -592,143 +593,3 @@ def _list_outputs(self):
 
 
 
-#
-##  Refinement HR mask
-# 
-
-
-class MialsrtkRefineHRMaskByIntersectionInputSpec(BaseInterfaceInputSpec):
-    bids_dir = Directory(desc='BIDS root directory',mandatory=True,exists=True)
-    input_images = InputMultiPath(File(desc='files to be SR', mandatory = True))
-    input_masks = InputMultiPath(File(desc='mask of files to be SR', mandatory = True))
-    input_transforms = InputMultiPath(File(desc='', mandatory = True))
-    input_sr = File(mandatory=True)
-
-    deblurring = traits.Bool(False)
-    out_LRmask_postfix = traits.Str("_LRmask", usedefault=True)
-    out_srmask_postfix = traits.Str("_srMask", usedefault=True)
-
-    stacksOrder = traits.List(mandatory = False)
-
-class MialsrtkRefineHRMaskByIntersectionOutputSpec(TraitedSpec):
-    output_SRmask = File()
-    output_LRmasks = OutputMultiPath(File())
-
-class MialsrtkRefineHRMaskByIntersection(BaseInterface):
-    input_spec = MialsrtkRefineHRMaskByIntersectionInputSpec
-    output_spec = MialsrtkRefineHRMaskByIntersectionOutputSpec
-
-    def _run_interface(self, runtime):
-
-        cmd = ['mialsrtkRefineHRMaskByIntersection']
-
-
-
-        run_nb_images  = []
-        for in_file in self.inputs.input_images:
-            cut_avt = in_file.split('run-')[1]
-            cut_apr = cut_avt.split('_')[0]
-            run_nb_images.append(int(cut_apr))
-
-        run_nb_masks  = []
-        for in_mask in self.inputs.input_masks:
-            cut_avt = in_mask.split('run-')[1]
-            cut_apr = cut_avt.split('_')[0]
-            run_nb_masks.append(int(cut_apr))
-
-        run_nb_transforms  = []
-        for in_mask in self.inputs.input_transforms:
-            cut_avt = in_mask.split('run-')[1]
-            cut_apr = cut_avt.split('_')[0]
-            run_nb_transforms.append(int(cut_apr))
-
-
-
-        for order in self.inputs.stacksOrder:
-            index_img = run_nb_images.index(order)
-            index_mask = run_nb_masks.index(order)
-            index_tranform = run_nb_transforms.index(order)
-
-            cmd += ['-i', self.inputs.input_images[index_img]]
-            cmd += ['-m', self.inputs.input_masks[index_mask]]
-            cmd += ['-t', self.inputs.input_transforms[index_tranform]]
-
-
-            _, name, ext = split_filename(self.inputs.input_images[index_img])
-            out_file = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_LRmask_postfix, ext)))
-            cmd += ['-O', out_file]
-
-        _, name, ext = split_filename(os.path.abspath(self.inputs.input_images[0]))
-        out_file = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_srmask_postfix, ext)))
-
-        cmd += ['-r', self.inputs.input_sr]
-        cmd += ['-o', out_file]
-        cmd += ['--radius-dilation', str(1)]
-
-
-
-        try:
-            print('... cmd: {}'.format(cmd))
-            cmd = ' '.join(cmd)
-            run(self, cmd, env={}, cwd=os.path.abspath(self.inputs.bids_dir))
-        except:
-            print('Failed')
-
-        return runtime
-
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        _, name, ext = split_filename(os.path.abspath(self.inputs.input_images[0]))
-        outputs['output_SRmask'] = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_srmask_postfix, ext)))
-        outputs['output_LRmasks'] = glob(os.path.abspath(''.join(["*", self.inputs.out_LRmask_postfix, ext])))
-        return outputs
-
-
-
-
-
-# 
-## N4 Bias field correction
-# 
-
-
-class MialsrtkN4BiasFieldCorrectionInputSpec(BaseInterfaceInputSpec):
-    bids_dir = Directory(desc='BIDS root directory',mandatory=True,exists=True)
-    input_image = File(desc='files to be HistNorm', mandatory = True)
-    input_mask = File(desc='mask of files to be HistNorm', mandatory = False)
-
-    out_im_postfix = traits.Str("_gbcorr", usedefault=True)
-    out_fld_postfix = traits.Str("_gbcorrfield", usedefault=True)
-
-
-class MialsrtkN4BiasFieldCorrectionOutputSpec(TraitedSpec):
-    output_image = File()
-    output_field = File()
-
-class MialsrtkN4BiasFieldCorrection(BaseInterface):
-    input_spec = MialsrtkN4BiasFieldCorrectionInputSpec
-    output_spec = MialsrtkN4BiasFieldCorrectionOutputSpec
-
-    def _run_interface(self, runtime):
-        _, name, ext = split_filename(os.path.abspath(self.inputs.input_image))
-        out_corr = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_im_postfix, ext)))
-        out_fld = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_fld_postfix, ext)))
-
-        cmd = ['mialsrtkN4BiasFieldCorrection', self.inputs.input_image, self.inputs.input_mask, out_corr, out_fld]
-
-        try:
-            print('... cmd: {}'.format(cmd))
-            cmd = ' '.join(cmd)
-            run(self, cmd, env={}, cwd=os.path.abspath(self.inputs.bids_dir))
-        except:
-            print('Failed')
-
-        return runtime
-
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        _, name, ext = split_filename(os.path.abspath(self.inputs.input_image))
-        outputs['output_image'] = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_im_postfix, ext)))
-        outputs['output_field'] = os.path.join(os.getcwd().replace(self.inputs.bids_dir,'/fetaldata'), ''.join((name, self.inputs.out_fld_postfix, ext)))
-
-        return outputs