rotational_minctracc .py has a numeric type comparison error when comparing world co-ordinates #45
Description
Hi everyone,
I've being to trying to match some of our microCT scans of E15 embryos to the init_model available at http://www.mouseimaging.ca/technologies/mouse_atlas/mouse_embryo_atlas.html to ultimately ensure that rotational_minctracc.py does not fail when it is called in the MBM.py pipeline.
These CT scans were 512 DICOM images (512X512 pixels) that were converted to a MINC volume using dcm2mnc. I've displayed the mincinfo of one of these volumes below:
mincinfo 1908016_kat243_e6_fov20_20190816_110850_111039.mnc
file: 1908016_kat243_e6_fov20_20190816_110850_111039.mnc
image: unsigned short 0 to 65535
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 512 -0.04 10.24
yspace 512 0.04 -10.24
xspace 512 0.04 -10.24
I also have to do some image processing on these scans to remove a undesired background stage (stage_labelledis a label volume where I manually segmented the stage) but this has no effects on mincinfo.
mincmath -clobber -div 1908016_kat243_e6_fov20_20190816_110850_111039.mnc correct_stage.mnc stage_labelled.mnc
mincmath -clobber -const2 0 100000 -clamp stage_labelled.mnc 190816_kat243_e6_KaX.mnc
mincinfo 190816_kat243_e6_KaX.mnc
file: 190816_kat243_e6_KaX.mnc
image: unsigned short 0 to 65535
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 512 -0.04 10.24
yspace 512 0.04 -10.24
xspace 512 0.04 -10.24
In comparison, both the model and mask that I am trying to convert/match our CT-scans to has the following properties:
mincinfo final_model.mnc
file: final_model.mnc
image: signed__ short -32768 to 32767
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 602 0.027 -15.0564
yspace 405 0.027 -8.6925
xspace 347 0.027 -5.11522
To get these volumes to match I am running the folllowing commands:
#convert our scans to the right resolution/steps
autocrop -clobber -signed -step 0.027 0.027 0.027 1908016_kat243_e6_fov20_20190816_110850_111039.mnc test_autocrop.mnc
mincinfo test_autocrop.mnc
mincinfo test_autocrop.mnc
file: test_autocrop.mnc
image: signed__ short -32768 to 32767
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 759 0.027 -10.2
yspace 759 0.027 -10.24
xspace 759 0.027 -10.24
#our raw scans contain embryos in different orientations. As such I need to use #rotational_minctracc which needs a mask . As such, I have copied and enlarged the mask to be (759 X 759 X 759) and attempted to run rotational_minctracc.py to align two separately autocropped embryos (test_autocrop.mnc and test_autocrop_target.mnc) but it results in the follwing error.
mincreshape -clobber -start 0,0,0 count 759,759,759 image_mask.mnc enlarged_mask.mnc
mincinfo enlarged_mask.mnc test_autocrop.mnc test_autocrop_target.mnc
file: enlarged_mask.mnc
image: signed__ short -32768 to 32767
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 759 0.027 -15.0564
yspace 759 0.027 -8.6925
xspace 759 0.027 -5.11522
file: test_autocrop.mnc
image: unsigned short 0 to 65535
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 759 0.027 -10.2
yspace 759 0.027 -10.24
xspace 759 0.027 -10.24
file: test_autocrop_target.mnc
image: unsigned short 0 to 65535
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 759 0.027 -10.2
yspace 759 0.027 -10.24
xspace 759 0.027 -10.24
rotational_minctracc.py -m enlarged_mask.mnc test_autocrop.mnc test_autocrop_target.mnc test_minc_trans.fxm test_minc_vol.mnc
TMP: /tmp/
RANGE: 50 INTERVAL: 10
[autocrop] [minc@mincvm:/media/sf_vmshare/Kat_crp_mnc] [2019-09-21 04:25:31] /opt/minc/1.9.17/bin/mincresample test_autocrop.mnc //tmp//rot_17719/rot_0..mnc -start -10.24 -10.24 -10.2 -step 0.2 0.2 0.2 -nelements 103 103 103
Transforming slices:.......................................................................................................Done
[autocrop] [minc@mincvm:/media/sf_vmshare/Kat_crp_mnc] [2019-09-21 04:25:42] /opt/minc/1.9.17/bin/mincresample test_autocrop_target.mnc //tmp//rot_17719/rot_1.mnc -start -10.24 -10.24 -10.2 -step 0.2 0.2 0.2 -nelements 103 103 103
Transforming slices:.......................................................................................................Done
[autocrop] [minc@mincvm:/media/sf_vmshare/Kat_crp_mnc] [2019-09-21 04:25:53] /opt/minc/1.9.17/bin/mincresample enlarged_mask.mnc //tmp//rot_17719/rot_2.mnc -start -5.11522 -8.6925 -15.0564 -step 0.2 0.2 0.2 -nelements 103 103 103
Transforming slices:.......................................................................................................Done
Using positive peak threshold 7.2
Peaks found in the source image (Distance Transform):
[2.16 0.96 3.6 ]
[1.025 0.25 4.925]
[-2.84 -0.24 -4. ]
[ 0.24571429 -0.95428574 -2.7428572 ]
[-0.24 -1.04 -1.8 ]
[2.4933333 0.22666667 0.13333334]
Making byte volume...
Using positive peak threshold 3010.32
Peaks found in the source image (blurred image):
[ 0.56 1.76 -2.2 ]
[-1.24 1.16 -1. ]
[-1.44 1.76 -2.4 ]
[-0.84 -1.04 -1.2 ]
Using positive peak threshold 10.4
Peaks found in the target image (Distance Transform):
[-0.44 -1.44 4.8 ]
[-2.24 -1.24 4. ]
[-1.04 -1.84 5.4 ]
Making byte volume...
Using positive peak threshold 2963.95
Peaks found in the target image (blurrred image):
[ 0.36 2.16 -2.4 ]
[ 1.16 1.96 -0.8 ]
[ 0.16 -1.24 -2. ]
Transforming slices:.......................................................................................................Done
Files //tmp//rot_17719/rot_2.mnc and //tmp//rot_17719/rot_5.mnc have different start coordinates (zspace)
Traceback (most recent call last):
File "/opt/miniconda/bin/rotational_minctracc.py", line 4, in
import('pkg_resources').run_script('python-stuffs==0.1.24', 'rotational_minctracc.py')
File "/opt/miniconda/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/opt/miniconda/lib/python3.7/site-packages/pkg_resources/init.py", line 1460, in run_script
exec(script_code, namespace, namespace)
File "/opt/miniconda/lib/python3.7/site-packages/python_stuffs-0.1.24-py3.7.egg/EGG-INFO/scripts/rotational_minctracc.py", line 422, in
File "/opt/miniconda/lib/python3.7/site-packages/python_stuffs-0.1.24-py3.7.egg/EGG-INFO/scripts/rotational_minctracc.py", line 413, in main
File "/opt/miniconda/lib/python3.7/site-packages/python_stuffs-0.1.24-py3.7.egg/EGG-INFO/scripts/rotational_minctracc.py", line 240, in loop_rotations
File "/opt/miniconda/lib/python3.7/site-packages/python_stuffs-0.1.24-py3.7.egg/EGG-INFO/scripts/rotational_minctracc.py", line 162, in get_cross_correlation_from_coordinate_pair
File "/opt/miniconda/lib/python3.7/site-packages/python_stuffs-0.1.24-py3.7.egg/EGG-INFO/scripts/rotational_minctracc.py", line 108, in compute_xcorr
File "/opt/miniconda/lib/python3.7/subprocess.py", line 395, in check_output
**kwargs).stdout
File "/opt/miniconda/lib/python3.7/subprocess.py", line 487, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['minccmp', '-xcorr', '-mask', '//tmp//rot_17719/rot_2.mnc', '//tmp//rot_17719/rot_5.mnc', '//tmp//rot_17719/rot_1.mnc']' returned non-zero exit status 1.
To match the co-ordinates between volumes:
autocrop -signed -clobber -debug -from enlarged_mask.mnc test_autocrop.mnc test_world_coord.mnc
GetVolumeBounds:
xspace: start=-5.11522, stop=15.3508
yspace: start=-8.6925, stop=11.7735
zspace: start=-15.0564, stop=5.4096
GetTagBounds:
xspace: start=-5.11522, extent=20.493
yspace: start=-8.6925, extent=20.493
zspace: start=-15.0564, extent=20.493
FixBounds:
xspace: start=-5.11522, extent=20.52
yspace: start=-8.6925, extent=20.52
zspace: start=-15.0564, extent=20.52
ModifyBounds:
xspace: start=-5.11522, extent=20.52
yspace: start=-8.6925, extent=20.52
zspace: start=-15.0564, extent=20.52
Params: -start -180,57,190 -count 760,760,760
Dimension order: 2 1 0
Params: -dimrange zspace=-180,760 -dimrange yspace=57,760 -dimrange xspace=190,760
[autocrop] [minc@mincvm:/media/sf_vmshare/Kat_crp_mnc] [2019-09-21 03:36:19] /opt/minc/1.9.17/bin/mincreshape -clobber -signed test_autocrop.mnc test_world_coord.mnc -dimrange zspace=-180,760 -dimrange yspace=57,760 -dimrange xspace=190,760
Copying chunks:........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................Done.
autocrop -signed -clobber -debug -from enlarged_mask.mnc test_autocrop_target.mnc test_world_coord_target.mnc
GetVolumeBounds:
xspace: start=-5.11522, stop=15.3508
yspace: start=-8.6925, stop=11.7735
zspace: start=-15.0564, stop=5.4096
GetTagBounds:
xspace: start=-5.11522, extent=20.493
yspace: start=-8.6925, extent=20.493
zspace: start=-15.0564, extent=20.493
FixBounds:
xspace: start=-5.11522, extent=20.52
yspace: start=-8.6925, extent=20.52
zspace: start=-15.0564, extent=20.52
ModifyBounds:
xspace: start=-5.11522, extent=20.52
yspace: start=-8.6925, extent=20.52
zspace: start=-15.0564, extent=20.52
Params: -start -180,57,190 -count 760,760,760
Dimension order: 2 1 0
Params: -dimrange zspace=-180,760 -dimrange yspace=57,760 -dimrange xspace=190,760
[autocrop] [minc@mincvm:/media/sf_vmshare/Kat_crp_mnc] [2019-09-21 04:34:33] /opt/minc/1.9.17/bin/mincreshape -clobber -signed test_autocrop_target.mnc test_world_coord_target.mnc -dimrange zspace=-180,760 -dimrange yspace=57,760 -dimrange xspace=190,760
Copying chunks:........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................Done.
mincinfo enlarged_mask.mnc test_world_coord.mnc test_world_coord_target.mnc
mincinfo enlarged_mask.mnc test_world_coord.mnc test_world_coord_target.mnc
file: enlarged_mask.mnc
image: signed__ short -32768 to 32767
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 759 0.027 -15.0564
yspace 759 0.027 -8.6925
xspace 759 0.027 -5.11522
file: test_world_coord.mnc
image: signed__ short -32768 to 32767
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 760 0.027 -15.06
yspace 760 0.027 -8.701
xspace 760 0.027 -5.11
file: test_world_coord_target.mnc
image: signed__ short -32768 to 32767
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 760 0.027 -15.06
yspace 760 0.027 -8.701
xspace 760 0.027 -5.11
#running rotational minctracc on corrected start spaces
rotational_minctracc.py -m enlarged_mask.mnc test_world_coord.mnc test_world_coord_target.mnc test_minc_trans.fxm test_minc_vol.mnc
TMP: /tmp/
RANGE: 50 INTERVAL: 10
[autocrop] [minc@mincvm:/media/sf_vmshare/Kat_crp_mnc] [2019-09-21 04:42:33] /opt/minc/1.9.17/bin/mincresample test_world_coord.mnc //tmp//rot_17791/rot_0..mnc -start -5.11 -8.701 -15.06 -step 0.2 0.2 0.2 -nelements 103 103 103
Transforming slices:.......................................................................................................Done
[autocrop] [minc@mincvm:/media/sf_vmshare/Kat_crp_mnc] [2019-09-21 04:42:44] /opt/minc/1.9.17/bin/mincresample test_world_coord_target.mnc //tmp//rot_17791/rot_1.mnc -start -5.11 -8.701 -15.06 -step 0.2 0.2 0.2 -nelements 103 103 103
Transforming slices:.......................................................................................................Done
[autocrop] [minc@mincvm:/media/sf_vmshare/Kat_crp_mnc] [2019-09-21 04:42:54] /opt/minc/1.9.17/bin/mincresample enlarged_mask.mnc //tmp//rot_17791/rot_2.mnc -start -5.11522 -8.6925 -15.0564 -step 0.2 0.2 0.2 -nelements 103 103 103
Transforming slices:.......................................................................................................Done
Using positive peak threshold 7.2
Peaks found in the source image (Distance Transform):
[2.19 0.899 3.64 ]
[-2.71 -0.301 -4.06 ]
[-0.05054054 -0.9496487 -2.2708108 ]
[2.39 0.299 0.34 ]
[2.64 1.449 1.19 ]
[2.59 0.399 1.74 ]
Making byte volume...
Using positive peak threshold 3020.42
Peaks found in the source image (blurred image):
[ 0.69 1.699 -2.26 ]
[-1.51 1.499 -2.26 ]
[-1.31 1.099 -1.06 ]
[-0.91 -0.901 -1.06 ]
[-1.11 -1.301 -1.66 ]
Using positive peak threshold 7.2
Peaks found in the target image (Distance Transform):
[-2.71 -1.101 1.54 ]
[-2.3570588 -1.5480589 3.4694118]
[ 3.54 0.499 -3.46 ]
[-2.51 0.499 1.14 ]
[-0.31 -1.9471538 3.8476923]
[-0.21 -0.601 3.94 ]
Making byte volume...
Using positive peak threshold 2945.38
Peaks found in the target image (blurrred image):
[ 0.29 2.099 -2.26 ]
[ 1.29 1.899 -0.86 ]
[ 0.09 -1.101 -1.86 ]
[ 1.89 -0.901 -1.66 ]
Transforming slices:.......................................................................................................Done
Files //tmp//rot_17791/rot_2.mnc and //tmp//rot_17791/rot_5.mnc have different start coordinates (zspace)
Traceback (most recent call last):
File "/opt/miniconda/bin/rotational_minctracc.py", line 4, in
import('pkg_resources').run_script('python-stuffs==0.1.24', 'rotational_minctracc.py')
File "/opt/miniconda/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/opt/miniconda/lib/python3.7/site-packages/pkg_resources/init.py", line 1460, in run_script
exec(script_code, namespace, namespace)
File "/opt/miniconda/lib/python3.7/site-packages/python_stuffs-0.1.24-py3.7.egg/EGG-INFO/scripts/rotational_minctracc.py", line 422, in
File "/opt/miniconda/lib/python3.7/site-packages/python_stuffs-0.1.24-py3.7.egg/EGG-INFO/scripts/rotational_minctracc.py", line 413, in main
File "/opt/miniconda/lib/python3.7/site-packages/python_stuffs-0.1.24-py3.7.egg/EGG-INFO/scripts/rotational_minctracc.py", line 240, in loop_rotations
File "/opt/miniconda/lib/python3.7/site-packages/python_stuffs-0.1.24-py3.7.egg/EGG-INFO/scripts/rotational_minctracc.py", line 162, in get_cross_correlation_from_coordinate_pair
File "/opt/miniconda/lib/python3.7/site-packages/python_stuffs-0.1.24-py3.7.egg/EGG-INFO/scripts/rotational_minctracc.py", line 108, in compute_xcorr
File "/opt/miniconda/lib/python3.7/subprocess.py", line 395, in check_output
**kwargs).stdout
File "/opt/miniconda/lib/python3.7/subprocess.py", line 487, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['minccmp', '-xcorr', '-mask', '//tmp//rot_17791/rot_2.mnc', '//tmp//rot_17791/rot_5.mnc', '//tmp//rot_17791/rot_1.mnc']' returned non-zero exit status 1.