From 54ffb77a558586108c838bc427aa741c9e4095bf Mon Sep 17 00:00:00 2001
From: Johannes Stelzer <johannes.stelzer@tuebingen.mpg.de>
Date: Mon, 11 Mar 2019 16:17:43 +0100
Subject: [PATCH] fixed nifti headers if entry does not exist in vista
---
vviewer/VistaLoad.py | 77 +++++++++++++++++++++++++-------------------
1 file changed, 44 insertions(+), 33 deletions(-)
diff --git a/vviewer/VistaLoad.py b/vviewer/VistaLoad.py
index 6cc1929..46828e8 100644
--- a/vviewer/VistaLoad.py
+++ b/vviewer/VistaLoad.py
@@ -56,6 +56,8 @@ import re
#%% AUX
def get_property_str(header_img, str_property, repn_property="int"):
+ if header_img is None:
+ return -1
idx_begin = header_img.find(str_property)
if idx_begin == -1:
return -1
@@ -85,7 +87,7 @@ def get_subheader(header, section_demark):
#%% reader
-fp_input = "/home/morty/tmp/test.v"
+# fp_input = "/mnt/50tbd/gabriele/median_02.v"
def load_vista(fp_input):
@@ -206,55 +208,64 @@ def load_vista(fp_input):
#%% re-parse the header to get the complete header information
+ nii_loaded = nib.Nifti1Image(data, affine=np.eye(4))
mm = get_property_str(header_img, "voxel", "list")
+ nii_loaded.header.set_zooms(mm)
+ nii_loaded.header['pixdim'][4] = tr
+ nii_loaded.header.set_xyzt_units(xyz="mm", t="msec")
+
if dim == "4D":
mm.append(tdim)
#get s-form code
sform_code = get_property_str(header, "sform_code", "int")
+ if sform_code != -1:
+ nii_loaded.header['sform_code'] = sform_code
qform_code = get_property_str(header, "qform_code", "int")
+ if qform_code != -1:
+ nii_loaded.header['qform_code'] = qform_code
header_sform = get_subheader(header, "sform: image")
- offset_sform = get_property_str(header_sform, "data", "int") + last_idx_header
- length_sform = int(get_property_str(header_sform, "length", "int")/4)
- sform1D = np.frombuffer(raw, dtype=np.float32, count=length_sform, offset=offset_sform).byteswap()
- sform2D = np.reshape(sform1D, (4,4))
+ offset_sform = get_property_str(header_sform, "data", "int")
+ if offset_sform != -1:
+ offset_sform += last_idx_header
+ length_sform = int(get_property_str(header_sform, "length", "int")/4)
+ sform1D = np.frombuffer(raw, dtype=np.float32, count=length_sform, offset=offset_sform).byteswap()
+ sform2D = np.reshape(sform1D, (4,4))
+ nii_loaded.set_sform(sform2D)
header_dim = get_subheader(header, "dim: bundle")
- offset_dim = get_property_str(header_dim, "data", "int") + last_idx_header
- length_dim = int(get_property_str(header_dim, "length", "int")/4)
- dim1D = np.frombuffer(raw, dtype=np.float32, count=length_dim, offset=offset_dim)
-
+ offset_dim = get_property_str(header_dim, "data", "int")
+ if offset_sform != -1:
+ offset_sform += last_idx_header
+ length_dim = int(get_property_str(header_dim, "length", "int")/4)
+ dim1D = np.frombuffer(raw, dtype=np.float32, count=length_dim, offset=offset_dim)
+
header_pixdim = get_subheader(header, "pixdim: bundle")
- offset_pixdim= get_property_str(header_dim, "data", "int") + last_idx_header
- length_pixdim = int(get_property_str(header_dim, "length", "int")/4)
- pixdim1D = np.frombuffer(raw, dtype=np.float32, count=length_dim, offset=offset_dim)
-
-
+ offset_pixdim= get_property_str(header_dim, "data", "int")
+ if offset_sform != -1:
+ offset_sform += last_idx_header
+ length_pixdim = int(get_property_str(header_dim, "length", "int")/4)
+ pixdim1D = np.frombuffer(raw, dtype=np.float32, count=length_dim, offset=offset_dim)
+
+
header_qform = get_subheader(header, "qform: bundle")
- offset_qform = get_property_str(header_qform, "data", "int") + last_idx_header
- length_qform = int(get_property_str(header_qform, "length", "int")/4)
- qformdim1D = np.frombuffer(raw, dtype=np.float32, count=length_qform, offset=offset_qform)
- # quatern_b quatern_c quatern_d qoffset_x qoffset_y qoffset_z
+ offset_qform = get_property_str(header_qform, "data", "int")
+ if offset_sform != -1:
+ offset_sform += last_idx_header
+ length_qform = int(get_property_str(header_qform, "length", "int")/4)
+ qformdim1D = np.frombuffer(raw, dtype=np.float32, count=length_qform, offset=offset_qform)
+ nii_loaded.header['quatern_b'] = qformdim1D[0]
+ nii_loaded.header['quatern_c'] = qformdim1D[1]
+ nii_loaded.header['quatern_d'] = qformdim1D[2]
+ nii_loaded.header['qoffset_x'] = qformdim1D[3]
+ nii_loaded.header['qoffset_y'] = qformdim1D[4]
+ nii_loaded.header['qoffset_z'] = qformdim1D[5]
+ # quatern_b quatern_c quatern_d qoffset_x qoffset_y qoffset_z
- #%% convert to nii object... fill in data and header
- nii_loaded = nib.Nifti1Image(data, affine=np.eye(4))
- # import pdb; pdb.set_trace()
- nii_loaded.header.set_zooms(mm)
- nii_loaded.header['pixdim'][4] = tr
- nii_loaded.set_sform(sform2D)
- nii_loaded.header['qform_code'] = qform_code
- nii_loaded.header['qform_code'] = sform_code
- nii_loaded.header['quatern_b'] = qformdim1D[0]
- nii_loaded.header['quatern_c'] = qformdim1D[1]
- nii_loaded.header['quatern_d'] = qformdim1D[2]
- nii_loaded.header['qoffset_x'] = qformdim1D[3]
- nii_loaded.header['qoffset_y'] = qformdim1D[4]
- nii_loaded.header['qoffset_z'] = qformdim1D[5]
- nii_loaded.header.set_xyzt_units(xyz="mm", t="msec")
return nii_loaded
--
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