This repository contains the code necessary in order to reproduce the work contained in the submitted paper: "Segmentation of Nuclei in Histopathology Images by deep regression of the distance map".
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Having toruble with query of "Running the pipeline with synthetic data" #10
nextflow run dummydataset.nf --epoch 10 -c nextflow.config -resume
N E X T F L O W ~ version 21.04.3
Launching dummydataset.nf [drunk_curie] - revision: 2c82bdc18e
executor > local (2)
[d7/7078ce] process > DummyDataSet (1) [ 0%] 0 of 2
[- ] process > CreateTFRecords -
[- ] process > Training -
Error executing process > 'DummyDataSet (2)'
Caused by:
Process DummyDataSet (2) terminated with an error exit status (1)
Command executed:
executor > local (2)
[d7/7078ce] process > DummyDataSet (1) [100%] 2 of 2, failed: 2 ✘
[- ] process > CreateTFRecords -
[- ] process > Training -
Error executing process > 'DummyDataSet (2)'
Caused by:
Process DummyDataSet (2) terminated with an error exit status (1)
Command error:
Traceback (most recent call last):
File "DDSCreation.py", line 5, in
from Data.DataGenClass import DataGenMulti
ImportError: No module named Data.DataGenClass
Work dir:
/home/ali/DRFNS-master/work/d9/062563da64edd7ce062e7a7d3452f0
Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line
nextflow run dummydataset.nf --epoch 10 -c nextflow.config -resume N E X T F L O W ~ version 21.04.3 Launching
dummydataset.nf
[drunk_curie] - revision: 2c82bdc18e executor > local (2) [d7/7078ce] process > DummyDataSet (1) [ 0%] 0 of 2 [- ] process > CreateTFRecords - [- ] process > Training - Error executing process > 'DummyDataSet (2)'Caused by: Process
DummyDataSet (2)
terminated with an error exit status (1)Command executed:
executor > local (2) [d7/7078ce] process > DummyDataSet (1) [100%] 2 of 2, failed: 2 ✘ [- ] process > CreateTFRecords - [- ] process > Training - Error executing process > 'DummyDataSet (2)'
Caused by: Process
DummyDataSet (2)
terminated with an error exit status (1)Command executed:
python DDSCreation.py --path TNBC_NucleiSegmentation --output ./UNNormalized --test 10 --mu 127 --sigma 100 --sigma2 10 --normalized 1
Command exit status: 1
Command output: (empty)
Command error: Traceback (most recent call last): File "DDSCreation.py", line 5, in
from Data.DataGenClass import DataGenMulti
ImportError: No module named Data.DataGenClass
Work dir: /home/ali/DRFNS-master/work/d9/062563da64edd7ce062e7a7d3452f0
Tip: when you have fixed the problem you can continue the execution adding the option
-resume
to the run command line