Closed andreanans closed 1 year ago
Hi,
I'm trying to test pyseg (devel plugin) in Scipion 3.0 and am getting the following error. Is this related to my install? Thanks
0018: Extracting GraphMCF and NetFilament objects from tomograms 00019: Author: Antonio Martinez-Sanchez 00020: Date: Mon 26 Jul 2021 15:54:42 BST 00021: 00022: Options: 00023: STAR file with the segmentations: Runs/000002_ProtPySegPreSegParticles/extra/presegVesiclesCentered_pre.star 00024: Number of parallel processes: 4 00025: DisPerSe persistence threshold (csig): 0.01 00026: Sigma for gaussian pre-processing: 1.0 00027: Sigma for contrast enhancement: 10 00028: Skeleton smoothing factor: 3 00029: Data resolution: 0.687 nm/pixel 00030: Mask offset: 0.0 nm 00031: Output directory: Runs/000113_ProtPySegGraphs/extra 00032: Graph density thresholds: 00033: Target vertex density (membrane) 0.0035 vertex/nm^3 for topological simplification 00034: Target edge/vertex ratio (non membrane) 4.0 for property field_value with mode low 00035: 00036: Paring input star file... 00037: Running main loop in parallel: 00038: P[2] Sub-volume to process found: Runs/000002_ProtPySegPreSegParticles/extra/segs/Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED_tid_2.mrc 00039: P[2] Computing paths for Runs/000002_ProtPySegPreSegParticles/extra/segs/Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED_tid_2.mrc ... 00040: P[2] Loading input data: Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED_tid_2.mrc 00041: P[2] Computing distance, mask and segmentation tomograms... 00042: P[2] Smoothing input tomogram (s=1.0)... 00043: P[2] Initializing DisPerSe... 00044: P[2] Persistence cut thereshold set to: 0.0004 grey level 00045: P[2] Running DisPerSe... *00046: Process Process-3: 00047: Traceback (most recent call last): 00048: File "/camp/home/nansa/.conda/envs/pySeg-jj_py3/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap 00049: self.run() 00050: File "/camp/home/nansa/.conda/envs/pySeg-jj_py3/lib/python3.6/multiprocessing/process.py", line 93, in run 00051: self._target(self._args, self._kwargs) 00052: File "/camp/apps/misc/stp/sbstp/scipion/3.0/software/em/pySeg-jj_py3/pyseg_system-jj_py3/code/tutorials/synth_sumb/tracing/mb_graph_mp.py", line 217, in pr_worker 00053: skel = disperse.get_skel() 00054: File "/camp/apps/misc/stp/sbstp/scipion/3.0/software/em/pySeg-jj_py3/pyseg_system-jj_py3/code/pyseg/disperse_io/handler.py", line 148, in get_skel 00055: raise pexceptions.PySegInputError(expr='get_skel (DisPerSe)', msg=error_msg) 00056: NameError: name 'pexceptions' is not defined****
Hi,
I'm trying to test pyseg (devel plugin) in Scipion 3.0 and am getting the following error. Is this related to my install? Thanks
0018: Extracting GraphMCF and NetFilament objects from tomograms 00019: Author: Antonio Martinez-Sanchez 00020: Date: Mon 26 Jul 2021 15:54:42 BST 00021:
00022: Options: 00023: STAR file with the segmentations: Runs/000002_ProtPySegPreSegParticles/extra/presegVesiclesCentered_pre.star 00024: Number of parallel processes: 4 00025: DisPerSe persistence threshold (csig): 0.01 00026: Sigma for gaussian pre-processing: 1.0 00027: Sigma for contrast enhancement: 10 00028: Skeleton smoothing factor: 3 00029: Data resolution: 0.687 nm/pixel 00030: Mask offset: 0.0 nm 00031: Output directory: Runs/000113_ProtPySegGraphs/extra 00032: Graph density thresholds: 00033: Target vertex density (membrane) 0.0035 vertex/nm^3 for topological simplification 00034: Target edge/vertex ratio (non membrane) 4.0 for property field_value with mode low 00035:
00036: Paring input star file... 00037: Running main loop in parallel: 00038: P[2] Sub-volume to process found: Runs/000002_ProtPySegPreSegParticles/extra/segs/Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED_tid_2.mrc 00039: P[2] Computing paths for Runs/000002_ProtPySegPreSegParticles/extra/segs/Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED_tid_2.mrc ... 00040: P[2] Loading input data: Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED_tid_2.mrc 00041: P[2] Computing distance, mask and segmentation tomograms... 00042: P[2] Smoothing input tomogram (s=1.0)... 00043: P[2] Initializing DisPerSe... 00044: P[2] Persistence cut thereshold set to: 0.0004 grey level 00045: P[2] Running DisPerSe... *00046: Process Process-3: 00047: Traceback (most recent call last): 00048: File "/camp/home/nansa/.conda/envs/pySeg-jj_py3/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap 00049: self.run() 00050: File "/camp/home/nansa/.conda/envs/pySeg-jj_py3/lib/python3.6/multiprocessing/process.py", line 93, in run 00051: self._target(self._args, self._kwargs) 00052: File "/camp/apps/misc/stp/sbstp/scipion/3.0/software/em/pySeg-jj_py3/pyseg_system-jj_py3/code/tutorials/synth_sumb/tracing/mb_graph_mp.py", line 217, in pr_worker 00053: skel = disperse.get_skel() 00054: File "/camp/apps/misc/stp/sbstp/scipion/3.0/software/em/pySeg-jj_py3/pyseg_system-jj_py3/code/pyseg/disperse_io/handler.py", line 148, in get_skel 00055: raise pexceptions.PySegInputError(expr='get_skel (DisPerSe)', msg=error_msg) 00056: NameError: name 'pexceptions' is not defined****