Open fjchichon opened 6 years ago
Dear @fjchichon, thanks for sharing this script!
When you talk about Stack of Micrographs...are you thinking in TiltSeries? My idea is to start testing the design of the data model for tomo. @cossorzano already had a good document that we can start with, but with some stuff from x-ray tomo that we might want to clean up first.
Can you explain (briefly, in text) what you scripts does (without the details) and the basic protocols for tomo/subtomo that you would like to see in Scipion?
Dear @delarosatrevin, Would you be so kind to share the script from @cossorzano you mentioned? I would like to look into that topic.
Hi @n1kt0 , The script is shared already in the first post of this issue. I was talking about Tomography Data Model...but we haven't started the implementation yet...but we are going to start working on it soon.
Are you interested in testing/working with some pre-processing protocols for Tomography we are start to implement in Scipion?
Since I'm an computer scientist working in tomography and have experience with IMOD and other tomography tools like tools for subtomogram averaging I would also be interested to integrate or help to integrate that stuff, I need only to learn more of the architecture of scipion to implement it conforming to the architecture. Some pointers where to look are appreciated.
Input movies have the name xxxxx_YYY[angle]_Fractions.mrc
where xxxxx is fixed string, YYY is a 3 digit number that identifies the movie and angle is the acquisition tilt angle.
(@delarosatrevin, @rmarabini mention to me that you are working in the tomograpy data model and you may be interested in knowing this request)
I enclosed a script creates the stacks:
!/bin/bash
FOLDERS
ROOTFOLDER=/HOME2/2018_02_27_fcojavierchichon_t7_tomo INPUTFOLDER=$ROOTFOLDER/GRID_09/DATA IMODFOLDER=$ROOTFOLDER/IMOD
if [ -d $IMODFOLDER ]; then echo "$IMODFOLDER exist" else mkdir $IMODFOLDER fi
echo $ROOTFOLDER echo $INPUTFOLDER
BUCLE======================
cd $INPUTFOLDER for i in T7php??.txt;do
VALIABLES 1---------
name=${i%.*} TOMOFOLDER=$IMODFOLDER/${name}
____
CREATE FOLDERS
if [ -d $TOMOFOLDER ]; then echo "directory $TOMOFOLDER exist" else mkdir $TOMOFOLDER fi
_____
VARIABLES DEPENDING ON DE TOMOGRAM
TOMO number
TOTAL_tilts=
ls $INPUTFOLDER/${name}*_Fractions_aligned_mic.mrc | wc -l
NEGtilts=`ls $INPUTFOLDER/${name}???[-*_Fractions_aligned_mic.mrc | wc -lPOS_tilts=
echo "$[TOTAL_tilts - NEG_tilts -1]"`TOMO files array
NEGfiles=`ls -r $INPUTFOLDER/${name}???[-_Fractions_aligned_mic.mrc
ZERO_file=
ls $INPUTFOLDER/${name}_001_Fractions_aligned_mic.mrcPOS_files=
ls $INPUTFOLDER/${name}_*_Fractions_aligned_mic.mrc | tail -n $POS_tilts`CREATE SORTED list para newstack and RAWTLT file fron namefiles
FIRST line number of lines=number of tilts
echo "$TOTAL_tilts" > $INPUTFOLDER/${name}_sorted.txt
RAWTLT genetation blank
if [ -e $TOMOFOLDER/${name}.rawtlt ]; then rm $TOMOFOLDER/${name}.rawtlt else touch $TOMOFOLDER/${name}.rawtlt fi
echo "" > $TOMOFOLDER/${name}.rawtlt
NEGATIVES
for file in $NEG_files; do
tilt_image
echo "$file" >> $INPUTFOLDER/${name}_sorted.txt
slice into file
echo "0" >> $INPUTFOLDER/${name}_sorted.txt
tiltfile
tilt=
echo $file | cut -d"[" -f 2 | cut -d"]" -f 1
echo "$tilt" >>$TOMOFOLDER/${name}.rawtlt doneZERO
echo $ZERO_file >> $INPUTFOLDER/${name}_sorted.txt
slice into file
echo "0" >> $INPUTFOLDER/${name}_sorted.txt tilt=
echo $ZERO_file | cut -d"[" -f 2 | cut -d"]" -f 1
echo "$tilt" >>$TOMOFOLDER/${name}.rawtltPOSITIVES (using tile -n POS_tilts
for file in $POS_files; do
tilt_image
echo "$file" >> $INPUTFOLDER/${name}_sorted.txt
slice into file
echo "0" >> $INPUTFOLDER/${name}_sorted.txt tilt=
echo $file | cut -d"[" -f 2 | cut -d"]" -f 1
echo "$tilt" >>$TOMOFOLDER/${name}.rawtlt doneGERERATE mrc STACKS with IMOD
if [ -e $TOMOFOLDER/corrected${name}.mrc ]; then rm $TOMOFOLDER/corrected${name}.mrc $TOMOFOLDER/${name}.st fi newstack -fileinlist $INPUTFOLDER/${name}sorted.txt $TOMOFOLDER/corrected${name}.mrc newstack -bin 2 $TOMOFOLDER/corrected_${name}.mrc $TOMOFOLDER/${name}.st
COPY Settings file to IMOD folders
cp $INPUTFOLDER/${name}.txt $TOMOFOLDER/${name}.txt
done