use brainpipe conda environment

PrincetonUniversity · Nov 18, 2021 · 49d4ffb · 49d4ffb
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commit 49d4ffb
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Showing 15 changed files with 34 additions and 181 deletions.
diff --git a/sub_registration_terastitcher.sh → example_tracing_pipeline.sh b/sub_registration_terastitcher.sh → example_tracing_pipeline.sh
@@ -17,23 +17,33 @@ cat /proc/meminfo
 echo "Array Allocation Number: $SLURM_ARRAY_JOB_ID"
 echo "Array Index: $SLURM_ARRAY_TASK_ID"
 
-
-module load anacondapy/5.3.1
-module load elastix/4.8
-. activate lightsheet
+module load anacondapy/2020.11
+. activate brainpipe
 
 #set up dictionary and save
 OUT0=$(sbatch --array=0 slurm_files/step0.sh) 
 echo $OUT0
 
-#process zplns, check that 1000 > zplns/slurmfactor
+#process zplns, assumes with tracing you are using terastitcher
 OUT1=$(sbatch --dependency=afterany:${OUT0##* } --array=0-2 slurm_files/step1.sh) 
 echo $OUT1
 
 #combine stacks into single tifffiles
 OUT2=$(sbatch --dependency=afterany:${OUT1##* } --array=0-3 slurm_files/step2.sh) 
 echo $OUT2
 
+#generate memmap array of full size cell channel data
+OUT4=$(sbatch --dependency=afterany:${OUT1##* } slurm_files/cnn_step0.sh "`pwd`") 
+echo $OUT4
+
+#generate chunks for cnn input
+OUT5=$(sbatch --dependency=afterany:${OUT4##* } --array=0-130 slurm_files/cnn_step1.sh "`pwd`") 
+echo $OUT5
+
+#check if correct number of patches were made
+OUT6=$(sbatch --dependency=afterany:${OUT5##* } slurm_files/cnn_step1_check.sh "`pwd`") 
+echo $OUT6
+
 #run elastix
 OUT3=$(sbatch --dependency=afterany:${OUT2##* } --array=0-2 slurm_files/step3.sh) 
 echo $OUT3
@@ -43,4 +53,4 @@ echo $OUT3
 # after = go once the specified job starts
 # afterany = go if the specified job finishes, regardless of success
 # afternotok = go if the specified job fails
-# afterok = go if the specified job completes successfully
+# afterok = go if the specified job completes successfully
diff --git a/registration_pipeline.sh b/registration_pipeline.sh
diff --git a/slurm_files/cnn_postprocess.sh b/slurm_files/cnn_postprocess.sh
@@ -13,8 +13,8 @@ echo "on host: `hostname` "
 cat /proc/$$/status | grep Cpus_allowed_list
 cat /proc/meminfo
 
-module load anacondapy/5.3.1
-. activate lightsheet
+module load anacondapy/2020.11
+. activate brainpipe
 
 #generate memmap array of reconstructed cnn output
 OUT0=$(sbatch slurm_files/cnn_step21.sh "`pwd`") 

diff --git a/slurm_files/cnn_preprocess.sh b/slurm_files/cnn_preprocess.sh
@@ -13,8 +13,8 @@ echo "on host: `hostname` "
 cat /proc/$$/status | grep Cpus_allowed_list
 cat /proc/meminfo
 
-module load anacondapy/5.3.1
-. activate lightsheet
+module load anacondapy/2020.11
+. activate brainpipe
 
 echo "Experiment name:" "`pwd`"
 

diff --git a/slurm_files/cnn_step0.sh b/slurm_files/cnn_step0.sh
@@ -14,8 +14,8 @@ echo "on host: `hostname` "
 
 cat /proc/$$/status | grep Cpus_allowed_list
 
-module load anacondapy/5.3.1
-. activate lightsheet
+module load anacondapy/2020.11
+. activate brainpipe
 
 echo "Experiment name:" "`pwd`"
 

diff --git a/slurm_files/cnn_step1.sh b/slurm_files/cnn_step1.sh
@@ -14,8 +14,8 @@ echo "on host: `hostname` "
 
 cat /proc/$$/status | grep Cpus_allowed_list
 
-module load anacondapy/5.3.1
-. activate lightsheet
+module load anacondapy/2020.11
+. activate brainpipe
 
 echo "Experiment name:" "`pwd`"
 echo "Array Index: $SLURM_ARRAY_TASK_ID"

diff --git a/slurm_files/cnn_step1_check.sh b/slurm_files/cnn_step1_check.sh
@@ -14,8 +14,8 @@ echo "on host: `hostname` "
 
 cat /proc/$$/status | grep Cpus_allowed_list
 
-module load anacondapy/5.3.1
-. activate lightsheet
+module load anacondapy/2020.11
+. activate brainpipe
 
 echo "Experiment name:" "`pwd`"
 echo "Array Index: $SLURM_ARRAY_TASK_ID"

diff --git a/slurm_files/cnn_step2.sh b/slurm_files/cnn_step2.sh
@@ -14,8 +14,8 @@ echo "on host: `hostname` "
 
 cat /proc/$$/status | grep Cpus_allowed_list
 
-module load anacondapy/5.3.1
-. activate lightsheet
+module load anacondapy/2020.11
+. activate brainpipe
 
 echo "Experiment name:" "`pwd`"
 

diff --git a/slurm_files/cnn_step21.sh b/slurm_files/cnn_step21.sh
@@ -14,8 +14,8 @@ echo "on host: `hostname` "
 
 cat /proc/$$/status | grep Cpus_allowed_list
 
-module load anacondapy/5.3.1
-. activate lightsheet
+module load anacondapy/2020.11
+. activate brainpipe
 
 echo "Experiment name:" "`pwd`"
 

diff --git a/slurm_files/cnn_step3.sh b/slurm_files/cnn_step3.sh
@@ -14,8 +14,8 @@ echo "on host: `hostname` "
 
 cat /proc/$$/status | grep Cpus_allowed_list
 
-module load anacondapy/5.3.1
-. activate lightsheet
+module load anacondapy/2020.11
+. activate brainpipe
 
 echo "Experiment name:" "`pwd`"
 echo "Array Index: $SLURM_ARRAY_TASK_ID"

diff --git a/slurm_files/cnn_step4.sh b/slurm_files/cnn_step4.sh
@@ -14,8 +14,8 @@ echo "on host: `hostname` "
 
 cat /proc/$$/status | grep Cpus_allowed_list
 
-module load anacondapy/5.3.1
-. activate lightsheet
+module load anacondapy/2020.11
+. activate brainpipe
 
 echo "Experiment name:" "`pwd`"
 

diff --git a/sub_registration.sh b/sub_registration.sh
diff --git a/sub_update_registration.sh b/sub_update_registration.sh
diff --git a/test_registration.sh b/test_registration.sh
diff --git a/tools/utils/directorydeterminer.py b/tools/utils/directorydeterminer.py
@@ -19,8 +19,6 @@ def directorydeterminer():
     """
     if socket.gethostname() == "spock-login.pni.princeton.edu":
         systemdirectory= "/jukebox/"
-    if socket.gethostname() == "PNI-1867vwtq2":
-        systemdirectory = "/jukebox/"
     else:
         systemdirectory = "/jukebox/"