20191022 23:03:47 (98) running [--augspeed 10 --models 1fm] [1] [0] [A] [4977] [10.7295/W9CDEEP3M3] on cil-cdeep3m-a-4977 20191022 23:03:47 (158) checking for /home/cdeep3m 20191022 23:03:47 (158) checking for /home/cdeep3m/images 20191022 23:03:47 (163) created /home/cdeep3m/images 20191022 23:03:47 (158) checking for /home/cdeep3m/8_bit 20191022 23:03:47 (163) created /home/cdeep3m/8_bit 20191022 23:03:47 (158) checking for /home/cdeep3m/train 20191022 23:03:47 (158) checking for /home/cdeep3m/predict 20191022 23:03:47 (163) created /home/cdeep3m/predict 20191022 23:03:47 (170) checking for model 10.7295/W9CDEEP3M3 20191022 23:03:47 (158) checking for /home/cdeep3m/train/10.7295 20191022 23:03:47 (158) checking for /home/cdeep3m/images/4977 20191022 23:03:47 (163) created /home/cdeep3m/images/4977 20191022 23:03:47 (275) fetching /home/cdeep3m/images/4977 from https://cildata.crbs.ucsd.edu/crop/4977/4977.tar 20191022 23:03:48 (232) [0]tar -xvf /home/cdeep3m/images/4977.tar -C /home/cdeep3m/images/4977 output2.000.tif output2.001.tif output2.002.tif output2.003.tif -----END extract_files----- 20191022 23:03:48 (249) getting https://microbial.crbs.ucsd.edu/Image_process_rest/crop_process_status/4977 20191022 23:03:48 (260) {"finished":false,"error":false,"message":"The image is cropped and it is launching the PRP POD now. The process ID is 4977","pod_running":"U"} 20191022 23:03:48 (128) A is the first!! {"finished":false,"error":false,"message":"The image is cropped and it is launching the PRP POD now. The process ID is 4977","pod_running":"U"} 20191022 23:03:48 (319) posting to https://microbial.crbs.ucsd.edu/Image_process_rest/report_running_pod/stage/4977/A -----START request----- 20191022 23:03:48 (329) Authorization: Basic Y2lsbWV0YTpCMzM2SHROTkZnYldpR2o= From: CDEEP3M_prp User-Agent: libwww-perl/6.15 Content-Length: 0 Content-Type: application/x-www-form-urlencoded 20191022 23:03:48 (330) application/x-www-form-urlencoded -----END request----- 20191022 23:03:48 (333) {"success":true} 20191022 23:03:48 (499) 4977 20191022 23:03:52 (502) [python3 /home/cdeep3m/functions/conv2uint8.py /home/cdeep3m/images/4977/ /home/cdeep3m/8_bit/4977/] 20191022 23:03:52 (503) [0][['/home/cdeep3m/functions/conv2uint8.py', '/home/cdeep3m/images/4977/', '/home/cdeep3m/8_bit/4977/'] Removing 5 percentile of grey values Processing 4 images Running 5 parallel tasks Loading: /home/cdeep3m/images/4977/output2.001.tif Saving: /home/cdeep3m/8_bit/4977/output2.001.tif /usr/local/lib/python3.5/dist-packages/skimage/util/dtype.py:135: UserWarning: Possible precision loss when converting from float64 to uint8 .format(dtypeobj_in, dtypeobj_out)) Loading: /home/cdeep3m/images/4977/output2.000.tif Saving: /home/cdeep3m/8_bit/4977/output2.000.tif /usr/local/lib/python3.5/dist-packages/skimage/util/dtype.py:135: UserWarning: Possible precision loss when converting from float64 to uint8 .format(dtypeobj_in, dtypeobj_out)) Loading: /home/cdeep3m/images/4977/output2.002.tif Saving: /home/cdeep3m/8_bit/4977/output2.002.tif /usr/local/lib/python3.5/dist-packages/skimage/util/dtype.py:135: UserWarning: Possible precision loss when converting from float64 to uint8 .format(dtypeobj_in, dtypeobj_out)) Loading: /home/cdeep3m/images/4977/output2.003.tif Saving: /home/cdeep3m/8_bit/4977/output2.003.tif /usr/local/lib/python3.5/dist-packages/skimage/util/dtype.py:135: UserWarning: Possible precision loss when converting from float64 to uint8 .format(dtypeobj_in, dtypeobj_out)) ] 20191022 23:03:52 (158) checking for /home/cdeep3m/predict/4977 20191022 23:03:52 (163) created /home/cdeep3m/predict/4977 20191022 23:03:52 (158) checking for /home/cdeep3m/predict/4977/logs 20191022 23:03:52 (163) created /home/cdeep3m/predict/4977/logs 20191022 23:04:39 (419) [/home/cdeep3m//runprediction.sh --augspeed 10 --models 1fm /home/cdeep3m/train/10.7295/W9CDEEP3M3/SEMTEM_membranes_TrainedNet /home/cdeep3m/8_bit/4977 /home/cdeep3m/predict/4977] 20191022 23:04:39 (420) [0][Starting Image Augmentation: Check image size of: /home/cdeep3m/8_bit/4977 Reading file: /home/cdeep3m/8_bit/4977/output2.000.tif Start up worker to generate packages to process Start up worker to run prediction on packages Start up worker to run post processing on packages To see progress run the following command in another window: tail -f /home/cdeep3m/predict/4977/logs/*.log Prediction has completed. Results are stored in /home/cdeep3m/predict/4977/ensembled Have a nice day! ] 20191022 23:04:39 (210) [0][in dir: /home/cdeep3m/predict/4977/1fm]tar -cvf /home/cdeep3m/predict/4977/1fm.tar * DONE Pkg001_Z01/ Pkg001_Z01/log/ Pkg001_Z01/DONE Pkg001_Z01/out.log Pkg001_Z01/cmdruns Pkg001_Z01/parallel.jobs Pkg001_Z01/PREDICTDONE Segmented_0001.png Segmented_0002.png Segmented_0003.png Segmented_0004.png -----END tar()----- 20191022 23:04:39 (348) sending /home/cdeep3m/predict/4977/1fm.tar to https://cildata.crbs.ucsd.edu/CIL-Storage-RS/index.php/Image_upload_service/upload_cdeep3m_other_files/4977 -----START request----- 20191022 23:04:39 (358) Authorization: Basic Y2lsc3RvcmU6aVUycDJEUUpjUnNmclhSNUJRbzg= From: CDEEP3M_prp User-Agent: libwww-perl/6.15 Content-Length: 1945722 Content-Type: multipart/form-data; boundary=xYzZY 20191022 23:04:39 (359) multipart/form-data; boundary=xYzZY -----END request----- 20191022 23:04:39 (363) { "success": true, "Full_path": "/export2/temp/cdeep3m_results/4977/others/1fm.tar", "URL": "https://cildata.crbs.ucsd.edu/cdeep3m_results/4977/others/1fm.tar" }20191022 23:04:40 (210) [0][in dir: /home/cdeep3m/predict/4977/ensembled]tar -cvf /home/cdeep3m/predict/4977/result.tar * DONE Pkg001_Z01/ Pkg001_Z01/log/ Pkg001_Z01/DONE Pkg001_Z01/out.log Pkg001_Z01/cmdruns Pkg001_Z01/parallel.jobs Pkg001_Z01/PREDICTDONE Segmented_0001.png Segmented_0002.png Segmented_0003.png Segmented_0004.png -----END tar()----- 20191022 23:04:40 (348) sending /home/cdeep3m/predict/4977/result.tar to https://cildata.crbs.ucsd.edu/CIL-Storage-RS/index.php/Image_upload_service/upload_cdeep3m_result/4977 -----START request----- 20191022 23:04:40 (358) Authorization: Basic Y2lsc3RvcmU6aVUycDJEUUpjUnNmclhSNUJRbzg= From: CDEEP3M_prp User-Agent: libwww-perl/6.15 Content-Length: 1945725 Content-Type: multipart/form-data; boundary=xYzZY 20191022 23:04:40 (359) multipart/form-data; boundary=xYzZY -----END request----- 20191022 23:04:40 (363) { "success": true, "Full_path": "/export2/temp/cdeep3m_results/4977/result/result.tar", "URL": "https://cildata.crbs.ucsd.edu/cdeep3m_results/4977/result/result.tar" }20191022 23:04:40 (158) checking for /home/cdeep3m/overlay 20191022 23:04:40 (163) created /home/cdeep3m/overlay 20191022 23:04:40 (158) checking for /home/cdeep3m/overlay/4977 20191022 23:04:40 (163) created /home/cdeep3m/overlay/4977 20191022 23:04:40 (482) processing output2.000.tif -- Segmented_0004.png 20191022 23:04:40 (485) python /home/cdeep3m/overlay.py /home/cdeep3m/8_bit/4977/output2.000.tif /home/cdeep3m/predict/4977/ensembled/Segmented_0001.png /home/cdeep3m/overlay/4977/overlay_001.png 20191022 23:04:43 (482) processing output2.001.tif -- Segmented_0003.png 20191022 23:04:43 (485) python /home/cdeep3m/overlay.py /home/cdeep3m/8_bit/4977/output2.001.tif /home/cdeep3m/predict/4977/ensembled/Segmented_0002.png /home/cdeep3m/overlay/4977/overlay_002.png 20191022 23:04:44 (482) processing output2.002.tif -- Segmented_0002.png 20191022 23:04:44 (485) python /home/cdeep3m/overlay.py /home/cdeep3m/8_bit/4977/output2.002.tif /home/cdeep3m/predict/4977/ensembled/Segmented_0003.png /home/cdeep3m/overlay/4977/overlay_003.png 20191022 23:04:45 (482) processing output2.003.tif -- Segmented_0001.png 20191022 23:04:45 (485) python /home/cdeep3m/overlay.py /home/cdeep3m/8_bit/4977/output2.003.tif /home/cdeep3m/predict/4977/ensembled/Segmented_0004.png /home/cdeep3m/overlay/4977/overlay_004.png 20191022 23:04:47 (210) [0][in dir: /home/cdeep3m/overlay/4977]tar -cvf /home/cdeep3m/overlay/4977/overlay.tar * overlay_001.png overlay_002.png overlay_003.png overlay_004.png -----END tar()----- 20191022 23:04:47 (348) sending /home/cdeep3m/overlay/4977/overlay.tar to https://cildata.crbs.ucsd.edu/CIL-Storage-RS/index.php/Image_upload_service/upload_preview_image/4977 -----START request----- 20191022 23:04:50 (358) Authorization: Basic Y2lsc3RvcmU6aVUycDJEUUpjUnNmclhSNUJRbzg= From: CDEEP3M_prp User-Agent: libwww-perl/6.15 Content-Length: 8192126 Content-Type: multipart/form-data; boundary=xYzZY 20191022 23:04:50 (359) multipart/form-data; boundary=xYzZY -----END request----- 20191022 23:04:50 (363) { "success": true, "Full_path": "/export2/temp/cdeep3m_results/4977/overlay/overlay.tar", "URL": "https://cildata.crbs.ucsd.edu/cdeep3m_results/4977/overlay/overlay.tar" }20191022 23:04:50 (104) time 1571785427 1571785490