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NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
Roy, I think you had a bad download. I got a valid netcdf-3 file, minc1-no-att.mnc, 6872 bytes. The full ncdump output is attached. I had to add -O and quoting to the curl command as originally shown, and remove the extra file name. I have no clue as to the original issue with scipy. --Dave On Fri, Jun 22, 2018 at 5:19 PM, Roy Mendelssohn - NOAA Federal < roy.mendelssohn@xxxxxxxx> wrote: > I downloaded the file. the standard "ncdump" from the netcdf library does > not view the file as a valid netcdf file. Therein lies your problem. > > -Roy > > > > On Jun 22, 2018, at 3:27 PM, Ankur Sinha <sanjay.ankur@xxxxxxxxx> wrote: > > > > Hello, > > > > While building nibabel for Fedora, we noticed a few tests failing when > > nibabel uses scipy.netcdf[1]. As the nibabel developers say there, the > > error does not occur with nibabel's bundled copy of netcdf.py, but it is > > easily reproducible with scipy's version: > > > > curl -L https://github.com/nipy/nibabel/blob/master/nibabel/ > tests/data/minc1-no-att.mnc?raw=true minc1-no-att.mnc > > python -c 'import scipy.io as sio; sio.netcdf_file("minc1-no-att.mnc")' > > > > Would someone please be able to have a look at the scipy issue[2] and > > provide some hints on where the bug may be? Unfortunately, we're not > > too well versed with netcdf to diagnose the issue ourselves. > > > > [1] https://github.com/nipy/nibabel/issues/579 > > [2] https://github.com/scipy/scipy/issues/8153 > > > > -- > > Thanks, > > Regards, > > > > Ankur Sinha "FranciscoD" > > > > https://fedoraproject.org/wiki/User:Ankursinha >
netcdf minc1-no-att {
dimensions:
zspace = 10 ;
yspace = 20 ;
xspace = 20 ;
variables:
int study ;
study:parent = "rootvariable" ;
study:varid = "MINC standard variable" ;
study:vartype = "group________" ;
study:version = "MINC Version 1.0" ;
study:modality = "MRI__" ;
int rootvariable ;
rootvariable:varid = "MINC standard variable" ;
rootvariable:vartype = "group________" ;
rootvariable:version = "MINC Version 1.0" ;
rootvariable:parent = "" ;
rootvariable:children = "study\n",
"image" ;
int zspace ;
zspace:varid = "MINC standard variable" ;
zspace:vartype = "dimension____" ;
zspace:version = "MINC Version 1.0" ;
zspace:comments = "Z increases from patient inferior to
superior" ;
zspace:spacing = "regular__" ;
zspace:alignment = "centre" ;
zspace:units = "mm" ;
zspace:spacetype = "native____" ;
int yspace ;
yspace:varid = "MINC standard variable" ;
yspace:vartype = "dimension____" ;
yspace:version = "MINC Version 1.0" ;
yspace:comments = "Y increases from patient posterior to
anterior" ;
yspace:spacing = "regular__" ;
yspace:alignment = "centre" ;
yspace:units = "mm" ;
yspace:spacetype = "native____" ;
int xspace ;
xspace:varid = "MINC standard variable" ;
xspace:vartype = "dimension____" ;
xspace:version = "MINC Version 1.0" ;
xspace:comments = "X increases from patient left to right" ;
xspace:spacing = "regular__" ;
xspace:alignment = "centre" ;
xspace:units = "mm" ;
xspace:spacetype = "native____" ;
double image-max ;
image-max:varid = "MINC standard variable" ;
image-max:vartype = "var_attribute" ;
image-max:version = "MINC Version 1.0" ;
image-max:_FillValue = 1. ;
image-max:parent = "image" ;
double image-min ;
image-min:varid = "MINC standard variable" ;
image-min:vartype = "var_attribute" ;
image-min:version = "MINC Version 1.0" ;
image-min:_FillValue = 0. ;
image-min:parent = "image" ;
byte image(zspace, yspace, xspace) ;
image:parent = "rootvariable" ;
image:varid = "MINC standard variable" ;
image:vartype = "group________" ;
image:version = "MINC Version 1.0" ;
image:image-max = "--->image-max" ;
image:image-min = "--->image-min" ;
image:complete = "true_" ;
image:signtype = "unsigned" ;
// global attributes:
:ident = "mb312:angela:2010.02.13.11.47.16:12472:1" ;
:minc_version = "2.3.00" ;
:history = "Tue Apr 16 19:15:53 2002>>> rawtominc -transverse
-byte -unsigned -range 0 255 -real_range 0 1 -orange 0 255 -xstep 2 -ystep 2
-zstep 2 -xstart -90 -ystart -126 -zstart -72 -xdircos 1 0 0 -ydircos 0 1 0
-zdircos 0 0 1 -mri canonical/avg152T1.mnc 91 109 91\n",
"Sat Feb 13 11:47:16 2010>>> mincresample
/home/mb312/opt/spm2/canonical/avg152T1.mnc test.mnc -nelements 20 20 10
-clobber -start -20 -20 -10\n",
"" ;
:_Format = "classic" ;
data:
study = 0 ;
rootvariable = _ ;
zspace = 0 ;
yspace = 0 ;
xspace = 0 ;
image-max = 0.7490196 ;
image-min = 0.2078431 ;
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}
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