use external (py)dcm2niix package

niftypet/nimpa/prc/imio.py

@@ -1,6 +1,5 @@
 """image input/output functionalities."""
 import datetime
-import glob
 import logging
 import os
 import pathlib
@@ -79,7 +78,7 @@ def getnii(fim, nan_replace=None, output='image'):
 
         # > get orientations from the affine
         ornt = nib.io_orientation(nim.affine)
-        trnsp = tuple(np.int8([ornt[2, 0],ornt[1, 0],ornt[0, 0]]))
+        trnsp = tuple(np.int8([ornt[2, 0], ornt[1, 0], ornt[0, 0]]))
         flip = tuple(np.int8(ornt[:, 1]))
 
         # > voxel size
@@ -252,29 +251,20 @@ def nii_gzip(imfile, outpath=''):
 
 def pick_t1w(mri):
     '''Pick the MR T1w from the dictionary for MR->PET registration.'''
-
-    if isinstance(mri, dict):
-        # check if NIfTI file is given
-        if 'T1N4' in mri and os.path.isfile(mri['T1N4']):
-            ft1w = mri['T1N4']
-        # or another bias corrected
-        elif 'T1bc' in mri and os.path.isfile(mri['T1bc']):
-            ft1w = mri['T1bc']
-        elif 'T1nii' in mri and os.path.isfile(mri['T1nii']):
-            ft1w = mri['T1nii']
-        elif 'T1DCM' in mri and os.path.exists(mri['MRT1W']):
-            # create file name for the converted NIfTI image
-            fnii = 'converted'
-            run([rs.DCM2NIIX, '-f', fnii, mri['T1nii']])
-            ft1nii = glob.glob(os.path.join(mri['T1nii'], '*converted*.nii*'))
-            ft1w = ft1nii[0]
-        else:
-            raise IOError('could not find a T1w image!')
-
-    else:
+    if not isinstance(mri, dict):
         raise IOError('incorrect input given for the T1w image')
 
-    return ft1w
+    # check if NIfTI file is given
+    if 'T1N4' in mri and os.path.isfile(mri['T1N4']):
+        return mri['T1N4']
+    # or another bias corrected
+    elif 'T1bc' in mri and os.path.isfile(mri['T1bc']):
+        return mri['T1bc']
+    elif 'T1nii' in mri and os.path.isfile(mri['T1nii']):
+        return mri['T1nii']
+    elif 'T1DCM' in mri and os.path.exists(mri['MRT1W']):
+        return dcm2nii(mri['T1nii'], 'converted')
+    raise IOError('could not find a T1w image!')
 
 
 # ======================================================================
@@ -921,59 +911,51 @@ def dcm2nii(
     fcomment='',
     outpath='',
     timestamp=True,
-    executable='',
+    executable=None,
     force=False,
 ):
-    '''
-    Convert DICOM files in folder (indicated by <dcmpth>) using DCM2NIIX
-    third-party software.
-    '''
+    """
+    Convert DICOM folder `dcmpth` to NIfTI using `dcm2niix` third-party software.
+    Args:
+      dcmpth: directory containing DICOM files
+    """
     # skip conversion if the output already exists and not force is selected
     if os.path.isfile(fimout) and not force:
         return fimout
 
-    if executable == '':
-        try:
-            executable = rs.DCM2NIIX
-        except AttributeError:
-            raise AttributeError('e> could not find variable DCM2NIIX in resources.py')
-    elif not os.path.isfile(executable):
-        raise IOError('e> the executable is incorrect!')
+    if not executable:
+        executable = getattr(rs, 'DCM2NIIX', None)
+        if not executable:
+            import dcm2niix
+            executable = dcm2niix.bin
+    if not os.path.isfile(executable):
+        raise IOError(f"executable not found:{executable}")
 
     if not os.path.isdir(dcmpth):
-        raise IOError('e> the provided DICOM path is not a folder!')
+        raise IOError("the provided `dcmpth` is not a folder")
 
-    # > output path
-    if outpath == '' and fimout != '' and '/' in fimout:
+    # output path
+    if not outpath and fimout and '/' in fimout:
         opth = os.path.dirname(fimout)
-        if opth == '':
-            opth = dcmpth
+        opth = opth or dcmpth
         fimout = os.path.basename(fimout)
-
-    elif outpath == '':
-        opth = dcmpth
-
     else:
-        opth = outpath
+        opth = outpath or dcmpth
 
     create_dir(opth)
 
-    if fimout == '':
+    if not fimout:
         fimout = fprefix
         if timestamp:
             fimout += time_stamp(simple_ascii=True)
-
     fimout = fimout.split('.nii')[0]
 
-    # convert the DICOM mu-map images to nii
     run([executable, '-f', fimout, '-o', opth, dcmpth])
-
-    fniiout = glob.glob(os.path.join(opth, '*' + fimout + '*.nii*'))
+    fniiout = list(pathlib.Path(opth).glob(f"*{fimout}*.nii*"))
 
     if fniiout:
-        return fniiout[0]
-    else:
-        raise ValueError('e> could not get the output file!')
+        return str(fniiout[0])
+    raise ValueError("could not find output nii file")
 
 
 def dcm2im(fpth):

niftypet/nimpa/prc/prc.py

@@ -8,7 +8,6 @@
 import pathlib
 import re
 import sys
-from glob import glob
 from subprocess import run
 from textwrap import dedent
 from warnings import warn
@@ -908,15 +907,8 @@ def centre_mass_img(img, output='mm'):
 
 
 # ==============================================================================
-def centre_mass_corr(
-        img,
-        Cnt=None, 
-        com=None,
-        flip=None,
-        outpath=None,
-        fcomment='_com-modified',
-        fout=None):
-
+def centre_mass_corr(img, Cnt=None, com=None, flip=None, outpath=None, fcomment='_com-modified',
+                     fout=None):
     """
     Image centre of mass correction. The O point is in the middle of the
     image centre of voxel value mass (e.g, radio-activity).
@@ -935,7 +927,7 @@ def centre_mass_corr(
     else:
         raise ValueError('unrecognised input image')
 
-    #------------------------------------------------------------------
+    # ------------------------------------------------------------------
     # [optional]
     # > applies if requested a radical correction of orientation by flipping
     if flip is not None:
@@ -944,8 +936,7 @@ def centre_mass_corr(
             imdct['im'] = imdct['im'][:, ::flip[0], ::flip[1], ::flip[2]]
         elif dimno == 3:
             imdct['im'] = imdct['im'][::flip[0], ::flip[1], ::flip[2]]
-    #------------------------------------------------------------------
-
+    # ------------------------------------------------------------------
 
     # > check if the dictionary of constants is given
     if Cnt is None:
@@ -1024,7 +1015,7 @@ def centre_mass_corr(
     # get a new NIfTI image for the perturbed MR
     imdata = innii.get_fdata()
     if flip is not None:
-        imdata = imdata[::flip[2],::flip[1],::flip[0],...]
+        imdata = imdata[::flip[2], ::flip[1], ::flip[0], ...]
     newnii = nib.Nifti1Image(imdata, mA, innii.header)
 
     fnew = os.path.join(opth, fnm)
@@ -1308,7 +1299,7 @@ def bias_field_correction(fmr, fimout='', outpath='', fcomment='_N4bias', execut
         outdct.setdefault('fim', [])
         outdct['fim'].append(fn4)
 
-    if len(outdct['fim'])==1:
+    if len(outdct['fim']) == 1:
         outdct['fim'] = outdct['fim'][0]
 
     return outdct
@@ -1384,11 +1375,7 @@ def mr2pet_rigid(fpet, mridct, Cnt, outpath='', fcomment='', rmsk=True, rfwhm=15
     elif 'T1bc' in mridct and os.path.isfile(mridct['T1bc']):
         ft1w = mridct['T1bc']
     elif 'T1DCM' in mridct and os.path.exists(mridct['MRT1W']):
-        # create file name for the converted NIfTI image
-        fnii = 'converted'
-        run([Cnt['DCM2NIIX'], '-f', fnii, mridct['T1nii']])
-        ft1nii = glob(os.path.join(mridct['T1nii'], '*converted*.nii*'))
-        ft1w = ft1nii[0]
+        ft1w = imio.dcm2nii(mridct['T1nii'], 'converted', executable=Cnt.get('DCM2NIIX', None))
     else:
         raise ValueError('disaster: no T1w image!')
 

setup.cfg

@@ -47,6 +47,7 @@ setup_requires=
     miutil[cuda]>=0.4.0
 install_requires=
     cuvec>=2.3.1
+    pydcm2niix>=1.0.20220116
     dipy>=1.3.0
     miutil[nii]>=0.4.2
     nibabel>=2.4.0

setup.py

@@ -51,25 +51,12 @@
 # get the current setup, if any
 Cnt = resources.get_setup()
 # check the installation of tools
-chck_tls = tls.check_version(Cnt, chcklst=["RESPATH", "REGPATH", "DCM2NIIX"])
+chck_tls = tls.check_version(Cnt, chcklst=["RESPATH", "REGPATH"])
 
 # -------------------------------------------
 # NiftyPET tools:
 # -------------------------------------------
 if "sdist" not in sys.argv or any(i in sys.argv for i in ["build", "bdist", "wheel"]):
-    # DCM2NIIX
-    if not chck_tls["DCM2NIIX"]:
-        # reply = tls.query_yesno("q> dcm2niix not found.\n   Install it?")
-        # if reply:
-        log.info(
-            dedent("""\
-            --------------------------------------------------------------
-            Installing dcm2niix ...
-            --------------------------------------------------------------"""))
-        Cnt = tls.install_tool("dcm2niix", Cnt)
-    # ---------------------------------------
-
-    # -------------------------------------------
     # NiftyReg
     if not chck_tls["REGPATH"] or not chck_tls["RESPATH"]:
         reply = True