better use of PYTHONPATH

ImageD11/nbGui/S3DXRD/run_astra_recon.py

@@ -18,15 +18,11 @@ def main(h5name, dsfile):
     # horrible workaround to include id11 code path
     import sys
 
-    id11_code_path = sys.argv[1]
-
-    sys.path.insert(0, id11_code_path)
-
     from ImageD11.sinograms.sinogram import read_h5, write_h5
     import ImageD11.sinograms.dataset
     import numpy as np
 
-    h5name = sys.argv[2]
-    dsfile = sys.argv[3]
+    h5name = sys.argv[1]
+    dsfile = sys.argv[2]
 
     main(h5name, dsfile)

ImageD11/nbGui/S3DXRD/run_mlem_recon.py

@@ -28,11 +28,7 @@ def main(h5name, ginc, dsfile, dest, nthreads):
 
 if __name__ == "__main__":
     # horrible workaround to include id11 code path
-    import sys
-
-    id11_code_path = sys.argv[1]
-
-    sys.path.insert(0, id11_code_path)
+    import sys    
 
     import numpy as np
     import h5py
@@ -41,10 +37,10 @@ def main(h5name, ginc, dsfile, dest, nthreads):
     from ImageD11.sinograms.sinogram import GrainSinogram
     import ImageD11.grain
 
-    h5name = sys.argv[2]
-    ginc = int(sys.argv[3])
-    dsfile = sys.argv[4]
-    dest = sys.argv[5]
-    nthreads = int(sys.argv[6])
+    h5name = sys.argv[1]
+    ginc = int(sys.argv[2])
+    dsfile = sys.argv[3]
+    dest = sys.argv[4]
+    nthreads = int(sys.argv[5])
 
     main(h5name, ginc, dsfile, dest, nthreads)

ImageD11/nbGui/S3DXRD/run_pbp_recon.py

@@ -1,29 +1,24 @@
 if __name__ == "__main__":
-    # horrible workaround to include id11 code path
-    import sys
-
-    id11_code_path = sys.argv[1]
-
-    sys.path.insert(0, id11_code_path)
 
+    import sys
     import ImageD11.sinograms.point_by_point
     import ImageD11.sinograms.dataset
     from ImageD11 import cImageD11
     import ast
 
-    dsfile = sys.argv[2]
-    hkltol = float(sys.argv[3])
-    fpks = float(sys.argv[4])
-    dstol = float(sys.argv[5])
-    etacut = float(sys.argv[6])
-    ifrac = float(sys.argv[7])
-    costol = float(sys.argv[8])
-    y0 = float(sys.argv[9])
-    symmetry = sys.argv[10]
-    foridx = [int(x) for x in ast.literal_eval(sys.argv[11])]
-    forgen = [int(x) for x in ast.literal_eval(sys.argv[12])]
-    uniqcut = float(sys.argv[13])
-    minpkint = int(sys.argv[14])
+    dsfile = sys.argv[1]
+    hkltol = float(sys.argv[2])
+    fpks = float(sys.argv[3])
+    dstol = float(sys.argv[4])
+    etacut = float(sys.argv[5])
+    ifrac = float(sys.argv[6])
+    costol = float(sys.argv[7])
+    y0 = float(sys.argv[8])
+    symmetry = sys.argv[9]
+    foridx = [int(x) for x in ast.literal_eval(sys.argv[10])]
+    forgen = [int(x) for x in ast.literal_eval(sys.argv[11])]
+    uniqcut = float(sys.argv[12])
+    minpkint = int(sys.argv[13])
 
     print('Loading dset')
     ds = ImageD11.sinograms.dataset.load(dsfile)
@@ -52,4 +47,4 @@
     pbp_object.setpeaks(cf_2d)
 
     print('Go for pbp')
-    pbp_object.point_by_point(ds.pbpfile, loglevel=3)
+    pbp_object.point_by_point(ds.pbpfile, loglevel=3)

ImageD11/nbGui/nb_utils.py

@@ -151,8 +151,8 @@ def prepare_mlem_bash(ds, grains, id11_code_path, n_simultaneous_jobs=50, cores_
 #SBATCH --cpus-per-task={cores_per_task}
 #
 date
-echo python3 {python_script_path} {id11_code_path} {grainsfile} $SLURM_ARRAY_TASK_ID {dsfile} {reconfile} {cores_per_task} > {log_path} 2>&1
-python3 {python_script_path} {id11_code_path} {grainsfile} $SLURM_ARRAY_TASK_ID {dsfile} {reconfile} {cores_per_task} > {log_path} 2>&1
+echo PYTHONPATH={id11_code_path} python3 {python_script_path} {grainsfile} $SLURM_ARRAY_TASK_ID {dsfile} {reconfile} {cores_per_task} > {log_path} 2>&1
+PYTHONPATH={id11_code_path} python3 {python_script_path} {grainsfile} $SLURM_ARRAY_TASK_ID {dsfile} {reconfile} {cores_per_task} > {log_path} 2>&1
 date
     """.format(outfile_path=outfile_path,
                errfile_path=errfile_path,
@@ -198,8 +198,8 @@ def prepare_astra_bash(ds, grainsfile, id11_code_path):
 #
 date
 module load cuda
-echo python3 {python_script_path} {id11_code_path} {grainsfile} {dsfile} > {log_path} 2>&1
-python3 {python_script_path} {id11_code_path} {grainsfile} {dsfile} > {log_path} 2>&1
+echo PYTHONPATH={id11_code_path} python3 {python_script_path} {grainsfile} {dsfile} > {log_path} 2>&1
+PYTHONPATH={id11_code_path} python3 {python_script_path} {grainsfile} {dsfile} > {log_path} 2>&1
 date
     """.format(outfile_path=outfile_path,
                errfile_path=errfile_path,
@@ -243,8 +243,8 @@ def prepare_pbp_bash(pbp_object, id11_code_path, minpkint):
 #
 date
 source /cvmfs/hpc.esrf.fr/software/packages/linux/x86_64/jupyter-slurm/latest/envs/jupyter-slurm/bin/activate
-echo python3 {python_script_path} {id11_code_path} {dsfile} {hkltol} {fpks} {dstol} {etacut} {ifrac} {costol} {y0} {symmetry} {foridx} {forgen} {uniqcut} {minpkint} > {log_path} 2>&1
-OMP_NUM_THREADS=1 python3 {python_script_path} {id11_code_path} {dsfile} {hkltol} {fpks} {dstol} {etacut} {ifrac} {costol} {y0} {symmetry} {foridx} {forgen} {uniqcut} {minpkint} > {log_path} 2>&1
+echo OMP_NUM_THREADS=1 PYTHONPATH={id11_code_path} python3 {python_script_path} {dsfile} {hkltol} {fpks} {dstol} {etacut} {ifrac} {costol} {y0} {symmetry} {foridx} {forgen} {uniqcut} {minpkint} > {log_path} 2>&1
+OMP_NUM_THREADS=1 PYTHONPATH={id11_code_path} python3 {python_script_path} {dsfile} {hkltol} {fpks} {dstol} {etacut} {ifrac} {costol} {y0} {symmetry} {foridx} {forgen} {uniqcut} {minpkint} > {log_path} 2>&1
 date
         """.format(outfile_path=outfile_path,
                    errfile_path=errfile_path,