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nieverge
scripts
Commits
5056bd13
Commit
5056bd13
authored
Jul 05, 2019
by
Adrian Nievergelt
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allow spaces in the subframe directory
parent
c7c82b53
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processing/mc2FromMDOC.py
processing/mc2FromMDOC.py
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processing/mc2FromMDOC.py
View file @
5056bd13
...
@@ -137,7 +137,7 @@ with open(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"), "w+") as scr
...
@@ -137,7 +137,7 @@ with open(os.path.join(mdocDir, inBaseName + "_alignFramesMC2.sh"), "w+") as scr
doseWeightParams
=
""
doseWeightParams
=
""
scriptFile
.
write
(
"echo Aligning frame stack %s
\n
"
%
(
os
.
path
.
join
(
subframesDir
,
imageParams
[
'filename'
])
))
scriptFile
.
write
(
"echo Aligning frame stack %s
\n
"
%
(
os
.
path
.
join
(
subframesDir
,
imageParams
[
'filename'
])
))
scriptFile
.
write
(
"MotionCor2-cuda%i -InMrc
%s -OutMrc %s
-Patch %i %i -InFmMotion 1 -Iter 30 -Tilt %f -FtBin %i -PixSize %f%s%s
\n\n
"
%
(
args
.
cudaVer
,
os
.
path
.
join
(
subframesDir
,
imageParams
[
'filename'
]),
os
.
path
.
join
(
alignedDir
,
imageParams
[
'filename'
]),
args
.
patchSize
,
args
.
patchSize
,
imageParams
[
'tiltangle'
],
args
.
binning
,
imageParams
[
'pixelspacing'
],
doseWeightParams
,
verboseString
)
)
scriptFile
.
write
(
"MotionCor2-cuda%i -InMrc
\"
%s
\"
-OutMrc
\"
%s
\"
-Patch %i %i -InFmMotion 1 -Iter 30 -Tilt %f -FtBin %i -PixSize %f%s%s
\n\n
"
%
(
args
.
cudaVer
,
os
.
path
.
join
(
subframesDir
,
imageParams
[
'filename'
]),
os
.
path
.
join
(
alignedDir
,
imageParams
[
'filename'
]),
args
.
patchSize
,
args
.
patchSize
,
imageParams
[
'tiltangle'
],
args
.
binning
,
imageParams
[
'pixelspacing'
],
doseWeightParams
,
verboseString
)
)
scriptFile
.
write
(
"echo Creating combined tilt series stack %s
\n
"
%
(
inBaseName
+
"_mc2.mrc"
))
scriptFile
.
write
(
"echo Creating combined tilt series stack %s
\n
"
%
(
inBaseName
+
"_mc2.mrc"
))
scriptFile
.
write
(
"source /sw/apps/imod/current/imodenv
\n
"
)
scriptFile
.
write
(
"source /sw/apps/imod/current/imodenv
\n
"
)
scriptFile
.
write
(
"newstack -fileinlist %s -output %s -tilt %s%s
\n\n
"
%
(
os
.
path
.
basename
(
stackFileName
),
inBaseName
+
"_mc2.mrc"
,
os
.
path
.
basename
(
tiltFileName
),
verboseString
))
scriptFile
.
write
(
"newstack -fileinlist %s -output %s -tilt %s%s
\n\n
"
%
(
os
.
path
.
basename
(
stackFileName
),
inBaseName
+
"_mc2.mrc"
,
os
.
path
.
basename
(
tiltFileName
),
verboseString
))
...
...
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