Merge pull request #58 from Julievkm/sig

fixed pydicom and depreciated scatter interpolation

niftypet/nipet/mmraux.py

@@ -36,9 +36,9 @@ def fwhm2sig(fwhm):
 def lm_pos(datain, Cnt):
     '''get the position of table and gantry offset from the DICOM list-mode file'''
     if 'lm_dcm' in datain and os.path.isfile(datain['lm_dcm']):
-        dhdr = dcm.read_file(datain['lm_dcm'])
+        dhdr = dcm.dcmread(datain['lm_dcm'])
     elif 'lm_ima' in datain and os.path.isfile(datain['lm_ima']):
-        dhdr = dcm.read_file(datain['lm_ima'])
+        dhdr = dcm.dcmread(datain['lm_ima'])
     else:
         log.error('DICOM list-mode data not found!')
         return None
@@ -91,9 +91,9 @@ def lm_pos(datain, Cnt):
 def hdr_lm(datain, Cnt):
     '''Get the headers from DICOM list-mode data file'''
     if 'lm_dcm' in datain and os.path.isfile(datain['lm_dcm']):
-        dhdr = dcm.read_file(datain['lm_dcm'])
+        dhdr = dcm.dcmread(datain['lm_dcm'])
     elif 'lm_ima' in datain and os.path.isfile(datain['lm_ima']):
-        dhdr = dcm.read_file(datain['lm_ima'])
+        dhdr = dcm.dcmread(datain['lm_ima'])
     else:
         log.error('DICOM list-mode data not found!')
         return None
@@ -226,9 +226,9 @@ def hmu_resample0(hmupos, parts, Cnt):
 
 def time_diff_norm_acq(datain):
     if 'lm_dcm' in datain and os.path.isfile(datain['lm_dcm']):
-        dcm_lm = dcm.read_file(datain['lm_dcm'])
+        dcm_lm = dcm.dcmread(datain['lm_dcm'])
     elif 'lm_ima' in datain and os.path.isfile(datain['lm_ima']):
-        dcm_lm = dcm.read_file(datain['lm_ima'])
+        dcm_lm = dcm.dcmread(datain['lm_ima'])
     else:
         log.error('dicom header of list-mode data does not exist.')
         return None

niftypet/nipet/mmrnorm.py

@@ -70,7 +70,7 @@ def get_components(datain, Cnt):
     # possible DICOM locations for the Interfile header
     nhdr_locations = [[0x29, 0x1010], [0x29, 0x1110]]
     # read the DICOM file
-    d = dcm.read_file(fnrm_hdr)
+    d = dcm.dcmread(fnrm_hdr)
 
     # if   d[0x0018, 0x1020].value == 'syngo MR B20P' or d[0x0018, 0x1020].value == 'syngo MR E11':
     #     nhdr = d[0x29,0x1010].value.decode()

niftypet/nipet/sct/mmrsct.py

@@ -10,7 +10,7 @@
 import nibabel as nib
 import numpy as np
 import scipy.ndimage as ndi
-from scipy.interpolate import interp2d
+from scipy.interpolate import interp2d, RectBivariateSpline
 from scipy.special import erfc
 
 from .. import mmr_auxe, mmraux, mmrnorm
@@ -335,8 +335,12 @@ def intrp_bsct(sct3d, Cnt, sctLUT, ssrlut, dtype=np.float32):
             sct2d = sct3d[0, si, jj, ii]
 
             z = np.vstack([sct2d[-1, :], sct2d])
-            f = interp2d(x, y, z, kind='cubic')
-            znew = f(xnew, ynew)
+            # > old scatter interpolation
+            # f = interp2d(x, y, z, kind='cubic')
+            # znew = f(xnew, ynew)
+            f = RectBivariateSpline(x, y, z.T)
+            ft = lambda xnew, ynew: f(xnew, ynew).T
+            znew = ft(xnew, ynew)
 
             # unroll
             znew = znew[jjnew, iinew]