def test_findGridSquaresNotUploaded(self):
allParams = json.loads(
open(
"/scisoft/pxsoft/data/cryoem/testRunData/20180423/allParams.json"
).read())
dictGridSquares = UtilsIcat.findGridSquaresNotUploaded(allParams)
pprint.pprint(dictGridSquares)
def tes_getStackTraceLog(self):
errorMessage = None
try:
print(1 / 0)
except:
errorMessage = UtilsIcat.getStackTraceLog()
print(errorMessage)
self.assertNotEquals(errorMessage, None)
def tes_uploadToIcat(self):
listFiles = [
"/data/visitor/mx2005/cm01/20171209/RAW_DATA/baseplate-epu-grid2/Images-Disc1/GridSquare_7259648/Data/FoilHole_7265309_Data_7264706_7264707_20171207_1704-10925.mrc",
]
directory = "/data/visitor/mx2005/cm01/20171209/RAW_DATA/baseplate-epu-grid2"
proposal = "id310009"
sample = "sample1"
dataSetName = "GridSquare_7259648_{0}".format(round(time.time()))
dictMetadata = {
"EM_amplitude_contrast": 0.0,
"EM_dose_initial": 1.0,
"EM_dose_per_frame": 2.0,
"EM_images_count": 3.0,
"EM_magnification": 4.0,
"EM_position_x": 5.0,
"EM_position_y": 6.0,
"EM_protein_acronym": 7.0,
"EM_sampling_rate": 8.0,
"EM_spherical_aberration": 9.0,
"EM_voltage": 10.0
}
UtilsIcat.uploadToIcat(listFiles, directory, proposal, sample,
dataSetName, dictMetadata)
def tes_uploadToIcat(self):
listFiles = [
"/data/visitor/mx415/cm01/20180619/RAW_DATA/epu-grid2-ddw49-1_1/Images-Disc1/GridSquare_7728190/Data/FoilHole_7742940_Data_7738968_7738969_20180611_0959.mrc"
]
directory = "/data/visitor/mx415/cm01/20180619/RAW_DATA/epu-grid2-ddw49-1_1"
proposal = "id000001"
sample = "Test"
dataSetName = "Test_1_1"
dictMetadata = {"EM_voltage": "300000"}
listGalleryPath = [
"/data/visitor/mx415/cm01/20180619/RAW_DATA/epu-grid2-ddw49-1_1/Images-Disc1/GridSquare_7728190/GridSquare_20180608_164247.jpg"
]
errorMessage = UtilsIcat.uploadToIcat(listFiles, directory, proposal,
sample, dataSetName,
dictMetadata, listGalleryPath)
print(errorMessage)
def archiveGridSquare(self, gridSquareToBeArchived):
# Archive remaining movies
self.info("Archiving grid square: {0}".format(gridSquareToBeArchived))
listPathsToBeArchived = []
sumPositionX = 0.0
sumPositionY = 0.0
indexPosition = 0
for movieName in self.allParams:
if "gridSquare" in self.allParams[movieName] and self.allParams[movieName]["gridSquare"] == gridSquareToBeArchived and not self.allParams[movieName]["archived"]:
listPathsToBeArchived.append(self.allParams[movieName]["movieFullPath"])
self.allParams[movieName]["archived"] = True
try:
sumPositionX += float(self.allParams[movieName]["positionX"])
sumPositionY += float(self.allParams[movieName]["positionY"])
indexPosition += 1
except:
pass
noImagesToBeArchived = len(listPathsToBeArchived)
if noImagesToBeArchived > 0:
if indexPosition > 0:
meanPositionX = sumPositionX / indexPosition
meanPositionY = sumPositionY / indexPosition
else:
meanPositionX = None
meanPositionY = None
dictIcatMetaData = dict(self.allParams["EM_meta_data"])
dictIcatMetaData["EM_position_x"] = meanPositionX
dictIcatMetaData["EM_position_y"] = meanPositionY
directory = dictIcatMetaData["EM_directory"]
listGalleryPath = self.allParams[gridSquareToBeArchived]["listGalleryPath"]
dataSetName = "{0}_{1}".format(gridSquareToBeArchived, round(time.time()))
self.allParams[dataSetName] = dictIcatMetaData
self.info("listPathsToBeArchived: {0}".format(pprint.pformat(listPathsToBeArchived)))
self.info("directory: {0}".format(directory))
self.info("self.proposal: {0}".format(self.proposal))
self.info("self.sampleAcronym: {0}".format(self.sampleAcronym))
self.info("dataSetName: {0}".format(dataSetName))
self.info("dictIcatMetaData: {0}".format(pprint.pformat(dictIcatMetaData)))
errorMessage = UtilsIcat.uploadToIcat(listPathsToBeArchived, directory, self.proposal,
self.sampleAcronym, dataSetName, dictIcatMetaData,
listGalleryPath)
if errorMessage is not None:
self.info("ERROR during icat upload!")
self.info(errorMessage)
def archiveOldGridSquares(self, gridSquareNotToArchive=None):
# Check if there are remaining grid squares to be uploaded:
dictGridSquares = UtilsIcat.findGridSquaresNotUploaded(self.allParams, gridSquareNotToArchive)
for gridSquareToBeArchived in dictGridSquares:
self.archiveGridSquare(gridSquareToBeArchived)