Mercurial > hg > orthanc-tests
annotate PerfsDb/DbPopulator.py @ 204:7a58288d1b27
fix
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 16 Jan 2019 09:17:03 +0100 |
| parents | 1ff0d830bb87 |
| children |
| rev | line source |
|---|---|
| 156 | 1 import typing |
| 161 | 2 import time |
| 163 | 3 import csv |
| 4 import os | |
| 156 | 5 from orthancRestApi import OrthancClient |
| 161 | 6 from TestResult import TestResult |
| 156 | 7 from DbSize import DbSize |
| 8 | |
| 9 class DbPopulator: | |
| 10 | |
| 11 def __init__(self, orthanc: OrthancClient, dbSize: DbSize): | |
| 12 self._orthanc = orthanc | |
| 13 self._dbSize = dbSize | |
| 14 self._sourceInstanceId = None | |
| 161 | 15 self._fileCounter = 0 |
| 16 | |
| 163 | 17 def populate(self, label: str): |
| 156 | 18 self._sourceInstanceId = self._orthanc.uploadDicomFile("../Database/DummyCT.dcm") |
| 19 | |
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20 if self._dbSize == DbSize.Tiny: |
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21 patientCount = 1 |
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22 smallStudiesPerPatient = 2 |
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23 largeStudiesPerPatient = 1 |
| 161 | 24 seriesPerSmallStudy = 1 |
| 25 seriesPerLargeStudy = 2 | |
| 26 instancesPerSmallSeries = 1 | |
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27 instancesPerLargeSeries = 5 |
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28 elif self._dbSize == DbSize.Small: |
| 161 | 29 patientCount = 100 |
| 156 | 30 smallStudiesPerPatient = 2 |
| 31 largeStudiesPerPatient = 1 | |
| 161 | 32 seriesPerSmallStudy = 1 |
| 33 seriesPerLargeStudy = 2 | |
| 34 instancesPerSmallSeries = 1 | |
| 35 instancesPerLargeSeries = 30 | |
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36 elif self._dbSize == DbSize.Medium: |
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37 patientCount = 1000 |
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38 smallStudiesPerPatient = 2 |
| 161 | 39 largeStudiesPerPatient = 2 |
| 40 seriesPerSmallStudy = 1 | |
| 41 seriesPerLargeStudy = 2 | |
| 42 instancesPerSmallSeries = 1 | |
| 43 instancesPerLargeSeries = 300 | |
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44 elif self._dbSize == DbSize.Large: |
| 161 | 45 patientCount = 10000 |
| 46 smallStudiesPerPatient = 2 | |
| 47 largeStudiesPerPatient = 2 | |
| 48 seriesPerSmallStudy = 1 | |
| 49 seriesPerLargeStudy = 2 | |
| 50 instancesPerSmallSeries = 1 | |
| 51 instancesPerLargeSeries = 300 | |
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52 else: |
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53 raise NotImplementedError |
| 156 | 54 |
| 161 | 55 print("Will generate data for (approximately):") |
| 56 print("{n:>12} patients".format(n=patientCount)) | |
| 57 print("{n:>12} studies".format(n=patientCount * (smallStudiesPerPatient + largeStudiesPerPatient))) | |
| 58 print("{n:>12} instances".format(n=patientCount * (smallStudiesPerPatient * seriesPerSmallStudy * instancesPerSmallSeries + largeStudiesPerPatient * seriesPerLargeStudy * instancesPerLargeSeries))) | |
| 59 | |
| 60 startTime = time.time() | |
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61 # first add data that are the same in small and large DBs (and that can be used in tests for comparing the same things !!) |
| 156 | 62 |
| 165 | 63 # used in TestFindStudyByPatientId100Results |
| 64 for i in range(100): | |
| 65 self.createStudy(studyIndex=199000+i, patientIndex=99997, seriesCount=1, instancesPerSeries=1) | |
| 66 | |
| 156 | 67 # used in TestFindStudyByPatientId5Results |
| 68 self.createStudy(studyIndex=99994, patientIndex=99998, seriesCount=1, instancesPerSeries=1) | |
| 69 self.createStudy(studyIndex=99995, patientIndex=99998, seriesCount=1, instancesPerSeries=1) | |
| 70 self.createStudy(studyIndex=99996, patientIndex=99998, seriesCount=1, instancesPerSeries=1) | |
| 71 self.createStudy(studyIndex=99997, patientIndex=99998, seriesCount=1, instancesPerSeries=1) | |
| 72 self.createStudy(studyIndex=99998, patientIndex=99998, seriesCount=1, instancesPerSeries=1) | |
| 73 | |
| 74 # used in TestFindStudyByStudyDescription1Result | |
| 75 # used in TestFindStudyByPatientId1Result | |
| 162 | 76 # used in TestToolsFindStudyByStudyInstanceUID |
| 156 | 77 self.createStudy(studyIndex=99999, patientIndex=99999, seriesCount=1, instancesPerSeries=1) |
| 78 | |
| 165 | 79 with open(os.path.join(os.path.dirname(os.path.abspath(__file__)), "Results/db-init-" + label + ".csv"), 'w', newline='') as resultFile: |
| 163 | 80 resultWriter = csv.writer(resultFile) |
| 165 | 81 resultWriter.writerow(["#patientCount", "filesCount", "files/sec"]) |
| 163 | 82 # then, add data to make the DB "large" or "small" |
| 83 for patientIndex in range(0, patientCount): | |
| 84 studyIndex=0 | |
| 85 print("Generating data for patient " + str(patientIndex)) | |
| 86 fileCounterAtPatientStart = self._fileCounter | |
| 87 startTimePatient = time.time() | |
| 88 | |
| 89 for i in range(0, smallStudiesPerPatient): | |
| 90 print("Generating small study " + str(i)) | |
| 91 self.createStudy(studyIndex=studyIndex, patientIndex=patientIndex, seriesCount=seriesPerSmallStudy, instancesPerSeries=instancesPerSmallSeries) | |
| 92 studyIndex+=1 | |
| 93 for i in range(0, largeStudiesPerPatient): | |
| 94 print("Generating large study " + str(i)) | |
| 95 self.createStudy(studyIndex=studyIndex, patientIndex=patientIndex, seriesCount=seriesPerLargeStudy, instancesPerSeries=instancesPerLargeSeries) | |
| 96 studyIndex+=1 | |
| 97 | |
| 98 endTimePatient = time.time() | |
| 99 print("STATS: uploaded {n} files in {s:.2f} seconds; {x:.2f} files/sec".format( | |
| 100 n=self._fileCounter - fileCounterAtPatientStart, | |
| 101 s=endTimePatient - startTimePatient, | |
| 102 x=(self._fileCounter - fileCounterAtPatientStart)/(endTimePatient - startTimePatient) | |
| 103 )) | |
| 104 resultWriter.writerow([ | |
| 105 patientIndex, | |
| 165 | 106 self._fileCounter, |
| 163 | 107 (self._fileCounter - fileCounterAtPatientStart)/(endTimePatient - startTimePatient) |
| 108 ]) | |
| 109 resultFile.flush() | |
| 156 | 110 |
| 161 | 111 endTime = time.time() |
| 112 print("Generation completed. Elapsed time: {duration:.2f} sec".format(duration=endTime-startTime)) | |
| 113 print("Uploaded {n} files -> {p:.2f} files/sec".format(n=self._fileCounter, p=self._fileCounter/(endTime-startTime))) | |
| 156 | 114 |
| 115 def createStudy(self, studyIndex: int, patientIndex: int, seriesCount: int, instancesPerSeries: int): | |
| 116 for seriesIndex in range(0, seriesCount): | |
| 117 for instanceIndex in range(0, instancesPerSeries): | |
| 118 dicomFile = self.createDicomFile(patientIndex=patientIndex, studyIndex=studyIndex, seriesIndex=seriesIndex, instanceIndex=instanceIndex) | |
| 119 self._orthanc.uploadDicom(dicomFile) | |
| 120 | |
| 121 def createDicomFile(self, patientIndex: int, studyIndex: int, seriesIndex: int, instanceIndex: int) -> object: | |
| 161 | 122 self._fileCounter += 1 |
| 156 | 123 return self._orthanc.instances.modify( |
| 124 instanceId=self._sourceInstanceId, | |
| 125 replaceTags={ | |
| 126 "PatientName": "Patient-" + str(patientIndex), | |
| 127 "PatientID": str(patientIndex), | |
| 128 "StudyDescription": str(patientIndex) + "-" + str(studyIndex), | |
| 129 "SeriesDescription": str(patientIndex) + "-" + str(studyIndex) + "-" + str(seriesIndex), | |
| 130 "SOPInstanceUID": str(patientIndex) + "." + str(studyIndex) + "." + str(seriesIndex) + "." + str(instanceIndex), | |
| 131 "StudyInstanceUID": str(patientIndex) + "." + str(studyIndex), | |
| 132 "SeriesInstanceUID": str(patientIndex) + "." + str(studyIndex) + "." + str(seriesIndex), | |
| 133 "SeriesNumber": str(seriesIndex), | |
| 134 "InstanceNumber": str(instanceIndex) | |
| 135 }, | |
| 136 deleteOriginal=False | |
| 137 ) |