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added current rcnn version, initial analysis tools
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‎.vscode/launch.json

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{
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// Use IntelliSense to learn about possible attributes.
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// Hover to view descriptions of existing attributes.
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// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
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"version": "0.2.0",
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"configurations": [
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{
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"name": "Python: Current File",
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"type": "python",
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"request": "launch",
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"program": "${file}",
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"console": "integratedTerminal",
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"cwd": "${fileDirname}"
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}
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]
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}

‎analysis/log_parser.py

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import matplotlib.pyplot as plt
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log_path = "../logs/"
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#filename = "log.traintest_03-18_17-08-23.3DCE 1 image 3 slice" #previous run, random 30%, no annealing, 10 epochs
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#filename = "log.traintest_04-16_08-08-30.3DCE 1 image 3 slice" #Smaller test run, 10 epochs 10% sampling
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filename = "log.traintest_04-16_09-45-43.3DCE 1 image 3 slice" #Latest run with sim_annealing, 10% sampling
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epoch=[]
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epoch_time=[]
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epoch_time_accumulated=[]
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epoch_validate=[]
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epochn=0
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fio = open(log_path+filename, "r")
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for line in fio:
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if 'Time cost' in line:
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#print(line)
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s = line.split('=')
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s[-1] = s[-1].strip() #remove the \n
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#print(s)
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epoch_time.append(float(s[1]))
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epoch.append(float(epochn))
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epochn=epochn+1
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if len(epoch_time_accumulated) == 0:
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epoch_time_accumulated.append(float(s[1]))
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else:
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epoch_time_accumulated.append(epoch_time_accumulated[-1]+float(s[1]))
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#Note: The validation criteria for 3DCE uses Sensitivity @ 4, in the log files.
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if 'Sensitivity' in line:
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#print(line)
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s=line.split(':')
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s[-1] = s[-1].strip() #remove the \n
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r = s[-1].split()
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#print(r)
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epoch_validate.append(float(r[3]))
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fio.close()
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print(epoch)
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print(epoch_time)
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print(epoch_time_accumulated)
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print(epoch_validate)
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plt.plot(epoch, epoch_validate)
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plt.ylabel('sensitivity')
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plt.xlabel('# of epochs')
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plt.show()
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plt.plot(epoch_time_accumulated, epoch_validate)
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plt.ylabel('sensitivity')
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plt.xlabel('epoch_time (s)')
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plt.show()

‎loadModules.sh

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#/bin/bash
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module unload python
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module load anaconda/Anaconda2
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module load cuda/9.0
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conda activate CADLab
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conda activate py2
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python --version

‎logs/log.traintest_03-18_14-15-13.3DCE 1 image 3 slice

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+ echo Logging output to '/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./log.traintest_03-18_14-15-13.3DCE 1 image 3 slice'
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Logging output to /home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./log.traintest_03-18_14-15-13.3DCE 1 image 3 slice
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+ python /home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./rcnn/tools/train.py
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Traceback (most recent call last):
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./rcnn/tools/train.py", line 15, in <module>
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from rcnn.core import callback, metric
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/core/callback.py", line 6, in <module>
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from rcnn.tools.validate import validate
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/tools/validate.py", line 4, in <module>
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from rcnn.tools.test import test_rcnn
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/tools/test.py", line 15, in <module>
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from rcnn.utils.load_data import filter_roidb
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/utils/load_data.py", line 55
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def sample_roidb(roidb, target)
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^
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SyntaxError: invalid syntax

‎logs/log.traintest_03-18_14-21-33.3DCE 1 image 3 slice

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‎logs/log.traintest_03-18_17-08-23.3DCE 1 image 3 slice

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‎logs/log.traintest_04-15_16-52-42.3DCE 1 image 3 slice

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+ echo Logging output to '/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./log.traintest_04-15_16-52-42.3DCE 1 image 3 slice'
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Logging output to /home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./log.traintest_04-15_16-52-42.3DCE 1 image 3 slice
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+ python /home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./rcnn/tools/train.py
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./rcnn/tools/train.py", line 225
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begin_epoch=args.begin_epoch, num_epoch=args.e2e_epoch, roidb)
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SyntaxError: non-keyword arg after keyword arg

‎logs/log.traintest_04-15_16-53-55.3DCE 1 image 3 slice

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+ echo Logging output to '/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./log.traintest_04-15_16-53-55.3DCE 1 image 3 slice'
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Logging output to /home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./log.traintest_04-15_16-53-55.3DCE 1 image 3 slice
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+ python /home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./rcnn/tools/train.py
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Traceback (most recent call last):
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./rcnn/tools/train.py", line 15, in <module>
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from rcnn.core import callback, metric
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/core/callback.py", line 6, in <module>
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from rcnn.tools.validate import validate
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/tools/validate.py", line 4, in <module>
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from rcnn.tools.test import test_rcnn
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/tools/test.py", line 12, in <module>
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from rcnn.core.tester import Predictor, pred_eval
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/core/tester.py", line 9, in <module>
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from module import MutableModule
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/core/module.py", line 230
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def fit(self, train_data,ogdb, eval_data=None, eval_metric='acc',
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SyntaxError: duplicate argument 'ogdb' in function definition

‎logs/log.traintest_04-15_16-56-12.3DCE 1 image 3 slice

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+ echo Logging output to '/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./log.traintest_04-15_16-56-12.3DCE 1 image 3 slice'
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Logging output to /home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./log.traintest_04-15_16-56-12.3DCE 1 image 3 slice
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+ python /home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./rcnn/tools/train.py
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/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/config.py:176: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
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yaml_cfg = edict(yaml.load(f))
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INFO:root:{'ANCHOR_RATIOS': [0.5, 1, 2],
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'ANCHOR_SCALES': [2, 3, 4, 6, 12],
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'CLASS_NAMES': ['bg', 'lesion'],
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'FIXED_PARAMS': [],
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'FIXED_PARAMS_SHARED': ['conv1', 'conv2', 'conv3', 'conv4', 'conv5'],
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'FRAMEWORK': '3DCE',
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'GT_MARGIN': 0,
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'IMAGE_STRIDE': 0,
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'IMG_DO_CLIP': True,
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'MAX_SIZE': 512,
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'NORM_SPACING': 0.8,
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'NUM_ANCHORS': 15,
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'NUM_CLASSES': 2,
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'NUM_IMAGES_3DCE': 1,
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'NUM_SLICES': 3,
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'PIXEL_MEANS': array([50]),
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'RCNN_FEAT_STRIDE': 8,
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'RPN_FEAT_STRIDE': 8,
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'SCALE': 512,
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'SLICE_INTV': 2,
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'TEST': {'CXX_PROPOSAL': False,
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'HAS_RPN': False,
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'NMS': 0.3,
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'PROPOSAL_MIN_SIZE': 8,
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'PROPOSAL_NMS_THRESH': 0.7,
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'PROPOSAL_POST_NMS_TOP_N': 2000,
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'PROPOSAL_PRE_NMS_TOP_N': 20000,
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'RPN_MIN_SIZE': 8,
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'RPN_NMS_THRESH': 0.7,
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'RPN_POST_NMS_TOP_N': 300,
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'RPN_PRE_NMS_TOP_N': 6000,
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'SAMPLES_PER_BATCH': 1},
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'TRAIN': {'ASPECT_GROUPING': False,
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'BATCH_ROIS': 32,
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'BBOX_MEANS': [0.0, 0.0, 0.0, 0.0],
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'BBOX_NORMALIZATION_PRECOMPUTED': True,
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'BBOX_NORMALIZE_TARGETS': False,
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'BBOX_REGRESSION_THRESH': 0.5,
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'BBOX_STDS': [0.1, 0.1, 0.2, 0.2],
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'BBOX_WEIGHTS': array([1., 1., 1., 1.]),
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'BG_THRESH_HI': 0.5,
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'BG_THRESH_LO': 0.0,
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'CXX_PROPOSAL': False,
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'END2END': True,
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'FG_FRACTION': 0.25,
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'FG_THRESH': 0.5,
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'RCNN_POS_UPSAMPLE': False,
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'RCNN_REG_LOSS_WEIGHT': 10,
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'RPN_BATCH_SIZE': 32,
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'RPN_BBOX_WEIGHTS': [1.0, 1.0, 1.0, 1.0],
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'RPN_CLOBBER_POSITIVES': False,
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'RPN_FG_FRACTION': 0.5,
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'RPN_MIN_SIZE': 8,
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'RPN_NEGATIVE_OVERLAP': 0.3,
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'RPN_NMS_THRESH': 0.7,
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'RPN_POSITIVE_OVERLAP': 0.7,
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'RPN_POSITIVE_WEIGHT': -1.0,
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'RPN_POST_NMS_TOP_N': 2000,
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'RPN_PRE_NMS_TOP_N': 12000,
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'RPN_REG_LOSS_WEIGHT': 1,
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'SAMPLES_PER_BATCH': 1},
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'WINDOWING': [-1024, 3071]}
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INFO:root:{'accs': {},
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'base_lr': 0.001,
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'begin_epoch': 0,
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'dataset': 'DeepLesion',
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'dataset_path': '/home/pulido/CADLab/lesion_detector_3DCE/images/',
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'e2e_epoch': 10,
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'e2e_lr': 0.001,
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'e2e_lr_step': '4,5',
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'e2e_prefix': 'model/3DCE 1 image 3 slice',
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'exp_name': '3DCE 1 image 3 slice',
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'flip': False,
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'frequent': 100,
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'gpus': '0',
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'groundtruth_file': '/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/data/DeepLesion/DL_info.csv',
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'image_path': '/home/pulido/CADLab/lesion_detector_3DCE/images/Images_png/',
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'image_set': 'train',
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'iter_size': 1,
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'keep_best_model': True,
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'kvstore': 'device',
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'lr_factor': 0.1,
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'network': 'vgg',
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'prefetch_thread_num': 4,
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'pretrained': '/home/pulido/CADLab/lesion_detector_3DCE/vgg16',
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'pretrained_epoch': 0,
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'proposal': 'rpn',
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'rand_seed': 23,
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'resume': False,
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'root_path': '/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/data',
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'show_avg_loss': 100,
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'shuffle': True,
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'test_image_set': 'test',
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'testing': False,
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'use_roidb_cache': True,
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'val_avg_fp': [0.5, 1, 2, 4, 8, 16],
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'val_gpu': '0',
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'val_has_rpn': True,
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'val_image_set': 'val',
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'val_iou_th': 0.5,
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'val_max_box': 5,
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'val_shuffle': False,
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'val_thresh': 0,
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'val_vis': False,
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'validate_at_begin': False,
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'weight_decay': 0.0005,
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'work_load_list': None}
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INFO:root:DeepLesion_train num_images 22496
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INFO:root:DeepLesion_train gt roidb loaded from /home/pulido/CADLab/lesion_detector_3DCE/images/cache/DeepLesion_train_gt_roidb.pkl
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INFO:root:noisy boxes filtered, images: 22496 -> 22478, bboxes: 22919 -> 22901
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INFO:root:sample boxes filtered, images: 22478 -> 224, bboxes: 22901 -> 22901
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INFO:root:Sampling 1 pcnt : 224 training slices
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INFO:root:Loading images with 4 threads.
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INFO:root:providing maximum shape [('data', (1, 3, 512, 512)), ('gt_boxes', (1, 5, 5))] [('label', (1, 61440)), ('bbox_target', (1, 60, 64, 64)), ('bbox_weight', (1, 60, 64, 64))]
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INFO:root:output shape {'bbox_loss_reshape_output': (1, 32, 8),
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'blockgrad0_output': (1, 32),
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'cls_prob_reshape_output': (1, 32, 2),
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'rpn_bbox_loss_output': (1, 60, 27, 16),
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'rpn_cls_prob_output': (1, 2, 405, 16)}
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INFO:root:loading parameters from /home/pulido/CADLab/lesion_detector_3DCE/vgg16-0000.params
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INFO:root:load param done
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INFO:root:lr 0.001000 lr_epoch_diff [4.0, 5.0] lr_iters [896, 1120]
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INFO:root:Epoch 0 Batch 0 19972876.2 smp/sec RPNLogLoss=0.743, RPNL1Loss=0.0142, RCNNLogLoss=0.694, RCNNL1Loss=1.44e-07,
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INFO:root:Epoch 0 Batch 100 10.0 smp/sec RPNLogLoss=0.288, RPNL1Loss=0.033, RCNNLogLoss=0.407, RCNNL1Loss=0.0395,
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INFO:root:Epoch 0 Batch 200 10.1 smp/sec RPNLogLoss=0.169, RPNL1Loss=0.0284, RCNNLogLoss=0.394, RCNNL1Loss=0.0752,
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INFO:root:Epoch[0] Train-RPNLogLoss=0.161003
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INFO:root:Epoch[0] Train-RPNL1Loss=0.021988
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INFO:root:Epoch[0] Train-RCNNLogLoss=0.408131
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INFO:root:Epoch[0] Train-RCNNL1Loss=0.079635
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INFO:root:Epoch[0] Time cost=22.339
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INFO:root:Saved checkpoint to "model/3DCE 1 image 3 slice-0001.params"
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INFO:root:Validating ...
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INFO:root:DeepLesion_val num_images 4793
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INFO:root:DeepLesion_val gt roidb loaded from /home/pulido/CADLab/lesion_detector_3DCE/images/cache/DeepLesion_val_gt_roidb.pkl
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INFO:root:noisy boxes filtered, images: 4793 -> 4791, bboxes: 4889 -> 4887
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INFO:root:Loading images with 4 threads.
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INFO:root:loading parameters from model/3DCE 1 image 3 slice-0001.params
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INFO:root:im_detect: 0/4791 data 0.065s im_detect 0.051s misc 0.004s
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INFO:root:im_detect: 200/4791 data 0.009s im_detect 0.047s misc 0.004s
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INFO:root:im_detect: 400/4791 data 0.009s im_detect 0.047s misc 0.004s
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600 800 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 4200 4400 4600
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Sensitivity @ [0.5, 1, 2, 4, 8, 16] average FPs per image: [0.00552486 0.01023123 0.0200532 0.0317168 0.05361162 0.08921629]
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Iter 1: 0.0317
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INFO:root:Validate callback: 0.031717
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INFO:root:Returned Validation=0.031717
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INFO:root:Retraining data=0.031717
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INFO:root:Loading images with 4 threads.
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INFO:root:Redoing training to meet criteria=1
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Traceback (most recent call last):
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./rcnn/tools/train.py", line 255, in <module>
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train_net(default)
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/./rcnn/tools/train.py", line 225, in train_net
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begin_epoch=args.begin_epoch, num_epoch=args.e2e_epoch)
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File "/home/pulido/CADLab/lesion_detector_3DCE/3DCE_new/rcnn/tools/../../rcnn/core/module.py", line 341, in fit
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sroidb = sample_roidb(ogdb, 10)
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NameError: global name 'sample_roidb' is not defined

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