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Feb 26, 2017
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ENH: support alternative header field name variants in .PAR files #507

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2c0555a
ENH: support some alternative header field name variants in .PAR files
grlee77 Jan 25, 2017
ff49a06
fix bad parrec test file
grlee77 Jan 26, 2017
47a8d6a
case of extension changed
grlee77 Jan 26, 2017
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8 changes: 8 additions & 0 deletions nibabel/parrec.py
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Original file line number Diff line number Diff line change
Expand Up @@ -206,6 +206,14 @@
'Max. number of gradient orients': ('max_gradient_orient', int),
# Line below added for par / rec version > 4.1
'Number of label types <0=no ASL>': ('nr_label_types', int),
# The following are duplicates of the above fields, but with slightly
# different abbreviation, spelling, or capatilization. Both variants have
# been observed in the wild in V4.2 PAR files:
# https://github.com/nipy/nibabel/issues/505
'Series_data_type': ('series_type',),
'Patient Position': ('patient_position',),
'Repetition time [msec]': ('repetition_time', float, None),
'Diffusion echo time [msec]': ('diffusion_echo_time', float),
}

# Image information as coded into a numpy structured array
Expand Down
128 changes: 128 additions & 0 deletions nibabel/tests/data/variant_v4_2_header.PAR
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Original file line number Diff line number Diff line change
@@ -0,0 +1,128 @@
# === DATA DESCRIPTION FILE ======================================================
#
# CAUTION - Investigational device.
# Limited by Federal Law to investigational use.
#
# Dataset name: E:\\Export\phantom_EPI_asc_CLEAR_2_1
#
# CLINICAL TRYOUT Research image export tool V4.2
#
# === GENERAL INFORMATION ========================================================
#
. Patient name : phantom
. Examination name : Konvertertest
. Protocol name : EPI_asc CLEAR
. Examination date/time : 2014.02.14 / 09:00:57
. Series_data_type : Image MRSERIES
. Acquisition nr : 2
. Reconstruction nr : 1
. Scan Duration [sec] : 14
. Max. number of cardiac phases : 1
. Max. number of echoes : 1
. Max. number of slices/locations : 9
. Max. number of dynamics : 3
. Max. number of mixes : 1
. Patient Position : HFS
. Preparation direction : Anterior-Posterior
. Technique : FEEPI
. Scan resolution (x, y) : 64 39
. Scan mode : MS
. Repetition time [msec] : 21225.76
. FOV (ap,fh,rl) [mm] : 240.000 70.000 240.000
. Water Fat shift [pixels] : 11.050
. Angulation midslice(ap,fh,rl)[degr]: -13.265 0.000 0.000
. Off Centre midslice(ap,fh,rl) [mm] : 2.508 30.339 -16.032
. Flow compensation <0=no 1=yes> ? : 0
. Presaturation <0=no 1=yes> ? : 0
. Phase encoding velocity [cm/sec] : 0.000000 0.000000 0.000000
. MTC <0=no 1=yes> ? : 0
. SPIR <0=no 1=yes> ? : 1
. EPI factor <0,1=no EPI> : 39
. Dynamic scan <0=no 1=yes> ? : 1
. Diffusion <0=no 1=yes> ? : 0
. Diffusion echo time [msec] : 0.00
. Max. number of diffusion values : 1
. Max. number of gradient orients : 1
#
# === PIXEL VALUES =============================================================
# PV = pixel value in REC file, FP = floating point value, DV = displayed value on console
# RS = rescale slope, RI = rescale intercept, SS = scale slope
# DV = PV * RS + RI FP = DV / (RS * SS)
#
# === IMAGE INFORMATION DEFINITION =============================================
# The rest of this file contains ONE line per image, this line contains the following information:
#
# slice number (integer)
# echo number (integer)
# dynamic scan number (integer)
# cardiac phase number (integer)
# image_type_mr (integer)
# scanning sequence (integer)
# index in REC file (in images) (integer)
# image pixel size (in bits) (integer)
# scan percentage (integer)
# recon resolution (x y) (2*integer)
# rescale intercept (float)
# rescale slope (float)
# scale slope (float)
# window center (integer)
# window width (integer)
# image angulation (ap,fh,rl in degrees ) (3*float)
# image offcentre (ap,fh,rl in mm ) (3*float)
# slice thickness (in mm ) (float)
# slice gap (in mm ) (float)
# image_display_orientation (integer)
# slice orientation ( TRA/SAG/COR ) (integer)
# fmri_status_indication (integer)
# image_type_ed_es (end diast/end syst) (integer)
# pixel spacing (x,y) (in mm) (2*float)
# echo_time (float)
# dyn_scan_begin_time (float)
# trigger_time (float)
# diffusion_b_factor (float)
# number of averages (integer)
# image_flip_angle (in degrees) (float)
# cardiac frequency (bpm) (integer)
# minimum RR-interval (in ms) (integer)
# maximum RR-interval (in ms) (integer)
# TURBO factor <0=no turbo> (integer)
# Inversion delay (in ms) (float)
# diffusion b value number (imagekey!) (integer)
# gradient orientation number (imagekey!) (integer)
# contrast type (string)
# diffusion anisotropy type (string)
# diffusion (ap, fh, rl) (3*float)
# label type (ASL) (imagekey!) (integer)
#
# === IMAGE INFORMATION ==========================================================
# sl ec dyn ph ty idx pix scan% rec size (re)scale window angulation offcentre thick gap info spacing echo dtime ttime diff avg flip freq RR-int turbo delay b grad cont anis diffusion L.ty

1 1 1 1 0 2 0 16 62 64 64 0.00000 1.29035 4.28404e-003 1070 1860 -13.26 -0.00 -0.00 2.51 -0.81 -8.69 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
2 1 1 1 0 2 1 16 62 64 64 0.00000 1.29035 4.28404e-003 1122 1951 -13.26 -0.00 -0.00 2.51 6.98 -10.53 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
3 1 1 1 0 2 2 16 62 64 64 0.00000 1.29035 4.28404e-003 1137 1977 -13.26 -0.00 -0.00 2.51 14.77 -12.36 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
4 1 1 1 0 2 3 16 62 64 64 0.00000 1.29035 4.28404e-003 1217 2116 -13.26 -0.00 -0.00 2.51 22.55 -14.20 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
5 1 1 1 0 2 4 16 62 64 64 0.00000 1.29035 4.28404e-003 1216 2113 -13.26 -0.00 -0.00 2.51 30.34 -16.03 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
6 1 1 1 0 2 5 16 62 64 64 0.00000 1.29035 4.28404e-003 1141 1983 -13.26 -0.00 -0.00 2.51 38.13 -17.87 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
7 1 1 1 0 2 6 16 62 64 64 0.00000 1.29035 4.28404e-003 1119 1945 -13.26 -0.00 -0.00 2.51 45.91 -19.70 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
8 1 1 1 0 2 7 16 62 64 64 0.00000 1.29035 4.28404e-003 1097 1907 -13.26 -0.00 -0.00 2.51 53.70 -21.54 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
9 1 1 1 0 2 8 16 62 64 64 0.00000 1.29035 4.28404e-003 1146 1991 -13.26 -0.00 -0.00 2.51 61.49 -23.37 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
1 1 2 1 0 2 9 16 62 64 64 0.00000 1.29035 4.28404e-003 1071 1863 -13.26 -0.00 -0.00 2.51 -0.81 -8.69 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
2 1 2 1 0 2 10 16 62 64 64 0.00000 1.29035 4.28404e-003 1123 1953 -13.26 -0.00 -0.00 2.51 6.98 -10.53 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
3 1 2 1 0 2 11 16 62 64 64 0.00000 1.29035 4.28404e-003 1135 1973 -13.26 -0.00 -0.00 2.51 14.77 -12.36 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
4 1 2 1 0 2 12 16 62 64 64 0.00000 1.29035 4.28404e-003 1209 2101 -13.26 -0.00 -0.00 2.51 22.55 -14.20 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
5 1 2 1 0 2 13 16 62 64 64 0.00000 1.29035 4.28404e-003 1215 2113 -13.26 -0.00 -0.00 2.51 30.34 -16.03 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
6 1 2 1 0 2 14 16 62 64 64 0.00000 1.29035 4.28404e-003 1145 1990 -13.26 -0.00 -0.00 2.51 38.13 -17.87 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
7 1 2 1 0 2 15 16 62 64 64 0.00000 1.29035 4.28404e-003 1119 1945 -13.26 -0.00 -0.00 2.51 45.91 -19.70 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
8 1 2 1 0 2 16 16 62 64 64 0.00000 1.29035 4.28404e-003 1093 1899 -13.26 -0.00 -0.00 2.51 53.70 -21.54 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
9 1 2 1 0 2 17 16 62 64 64 0.00000 1.29035 4.28404e-003 1150 1999 -13.26 -0.00 -0.00 2.51 61.49 -23.37 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
1 1 3 1 0 2 18 16 62 64 64 0.00000 1.29035 4.28404e-003 1070 1860 -13.26 -0.00 -0.00 2.51 -0.81 -8.69 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
2 1 3 1 0 2 19 16 62 64 64 0.00000 1.29035 4.28404e-003 1125 1955 -13.26 -0.00 -0.00 2.51 6.98 -10.53 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
3 1 3 1 0 2 20 16 62 64 64 0.00000 1.29035 4.28404e-003 1135 1973 -13.26 -0.00 -0.00 2.51 14.77 -12.36 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
4 1 3 1 0 2 21 16 62 64 64 0.00000 1.29035 4.28404e-003 1211 2105 -13.26 -0.00 -0.00 2.51 22.55 -14.20 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
5 1 3 1 0 2 22 16 62 64 64 0.00000 1.29035 4.28404e-003 1218 2118 -13.26 -0.00 -0.00 2.51 30.34 -16.03 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
6 1 3 1 0 2 23 16 62 64 64 0.00000 1.29035 4.28404e-003 1143 1987 -13.26 -0.00 -0.00 2.51 38.13 -17.87 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
7 1 3 1 0 2 24 16 62 64 64 0.00000 1.29035 4.28404e-003 1120 1947 -13.26 -0.00 -0.00 2.51 45.91 -19.70 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
8 1 3 1 0 2 25 16 62 64 64 0.00000 1.29035 4.28404e-003 1093 1901 -13.26 -0.00 -0.00 2.51 53.70 -21.54 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
9 1 3 1 0 2 26 16 62 64 64 0.00000 1.29035 4.28404e-003 1151 2001 -13.26 -0.00 -0.00 2.51 61.49 -23.37 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1

# === END OF DATA DESCRIPTION FILE ===============================================
14 changes: 14 additions & 0 deletions nibabel/tests/test_parrec.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,8 @@
# Fake varying scaling
VARY_PAR = pjoin(DATA_PATH, 'phantom_varscale.PAR')
VARY_REC = pjoin(DATA_PATH, 'phantom_varscale.REC')
# V4.2 PAR with variant field names in the header
VARIANT_PAR = pjoin(DATA_PATH, 'variant_v4_2_header.PAR')
# Affine as we determined it mid-2014
AN_OLD_AFFINE = np.array(
[[-3.64994708, 0., 1.83564171, 123.66276611],
Expand Down Expand Up @@ -829,3 +831,15 @@ def test_dualTR():
expected_TRs)
# zoom on 4th dimensions is the first TR (in seconds)
assert_equal(dualTR_hdr.get_zooms()[3], expected_TRs[0]/1000)


def test_alternative_header_field_names():
# some V4.2 files had variant spellings for some of the fields in the
# header. This test reads one such file and verifies that the fields with
# the alternate spelling were read.
with ImageOpener(VARIANT_PAR, 'rt') as _fobj:
HDR_INFO, HDR_DEFS = parse_PAR_header(_fobj)
assert_equal(HDR_INFO['series_type'], 'Image MRSERIES')
assert_equal(HDR_INFO['diffusion_echo_time'], 0.0)
assert_equal(HDR_INFO['repetition_time'], npa([ 21225.76]))
assert_equal(HDR_INFO['patient_position'], 'HFS')