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Merge pull request #507 from grlee77/parrec_keys
MRG: support alternative header field name variants in .PAR files This is a workaround for the alternative header naming variants observed in #505. I modified one of the existing .PAR files. I just truncated it and changed 4 header lines to have the entries from the .PAR file in #505. We can swap the file out for that other actual .par file prior to merging if the license terms permit.
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‎nibabel/parrec.py

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'Max. number of gradient orients': ('max_gradient_orient', int),
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# Line below added for par / rec version > 4.1
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'Number of label types <0=no ASL>': ('nr_label_types', int),
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# The following are duplicates of the above fields, but with slightly
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# different abbreviation, spelling, or capatilization. Both variants have
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# been observed in the wild in V4.2 PAR files:
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# https://github.com/nipy/nibabel/issues/505
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'Series_data_type': ('series_type',),
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'Patient Position': ('patient_position',),
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'Repetition time [msec]': ('repetition_time', float, None),
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'Diffusion echo time [msec]': ('diffusion_echo_time', float),
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}
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# Image information as coded into a numpy structured array

‎nibabel/tests/data/variant_v4_2_header.PAR

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

‎nibabel/tests/test_parrec.py

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# Fake varying scaling
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VARY_PAR = pjoin(DATA_PATH, 'phantom_varscale.PAR')
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VARY_REC = pjoin(DATA_PATH, 'phantom_varscale.REC')
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# V4.2 PAR with variant field names in the header
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VARIANT_PAR = pjoin(DATA_PATH, 'variant_v4_2_header.PAR')
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# Affine as we determined it mid-2014
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AN_OLD_AFFINE = np.array(
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[[-3.64994708, 0., 1.83564171, 123.66276611],
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expected_TRs)
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# zoom on 4th dimensions is the first TR (in seconds)
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assert_equal(dualTR_hdr.get_zooms()[3], expected_TRs[0]/1000)
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def test_alternative_header_field_names():
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# some V4.2 files had variant spellings for some of the fields in the
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# header. This test reads one such file and verifies that the fields with
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# the alternate spelling were read.
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with ImageOpener(VARIANT_PAR, 'rt') as _fobj:
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HDR_INFO, HDR_DEFS = parse_PAR_header(_fobj)
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assert_equal(HDR_INFO['series_type'], 'Image MRSERIES')
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assert_equal(HDR_INFO['diffusion_echo_time'], 0.0)
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assert_equal(HDR_INFO['repetition_time'], npa([ 21225.76]))
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assert_equal(HDR_INFO['patient_position'], 'HFS')

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