filepaths

Documentation

Index

• Constants
• func GetAnnotationsPath(userID string, datasetID string) string
• func GetCollectionPath(userID string, datasetID string, id string) string
• func GetConfigFilePath(fileName string) string
• func GetCustomImagePath(datasetID string, imgType string, fileName string) string
• func GetCustomMetaPath(datasetID string) string
• func GetDatasetFilePath(datasetID string, fileName string) string
• func GetDatasetListPath() string
• func GetDatasetSummaryFilePath(datasetID string) string
• func GetDatasetUploadPath(datasetID string, fileName string) string
• func GetDetectorConfigFilePath(configName string) string
• func GetDetectorConfigPath(configName string, version string, fileName string) string
• func GetElementSetPath(userID string) string
• func GetExpressionExecutionStatPath(exprID string) string
• func GetExpressionPath(userID string) string
• func GetJobDataPath(datasetID string, jobID string, fileName string) string
• func GetJobStatusPath(datasetID string, jobID string) string
• func GetJobSummaryPath(datasetID string) string
• func GetMultiQuantZStackPath(userID string, datasetID string) string
• func GetRGBMixPath(userID string) string
• func GetROIPath(userID string, datasetID string) string
• func GetSharedContentDatasetPath(datasetID string, fileName string) string
• func GetSharedQuantPath(datasetID string, fileName string) string
• func GetTagPath(userID string) string
• func GetUserContentDatasetPath(userID string, datasetID string, fileName string) string
• func GetUserContentPath(userID string, fileName string) string
• func GetUserLastPiquantOutputPath(userID string, datasetID string, piquantCommand string, fileName string) string
• func GetUserQuantPath(userID string, datasetID string, fileName string) string
• func GetViewStatePath(userID string, datasetID string, fileName string) string
• func GetWorkspacePath(userID string, datasetID string, id string) string
• func MakeQuantCSVFileName(quantID string) string
• func MakeQuantDataFileName(quantID string) string
• func MakeQuantLogDirName(quantID string) string
• func MakeQuantSummaryFileName(quantID string) string

Constants

const Auth0PemFileName = "auth0.pem"

----auth0.pem - Certificate needed by Auth0 to verify a user request is valid

const BadDatasetIDsFile = "bad-dataset-ids.json"

----bad-dataset-ids.json - Contains a list of Dataset IDs to ignore when generating dataset tiles. This is hand

maintained, only used when we have a bad dataset is downloaded that will never be usable
This way we can prevent it from being written to <Config bucket>/PixliseConfig/datasets.json

const CSVFileSuffix = ".csv"

CSVFileSuffix - CSV files are <jobid>.csv

const DatasetCustomMetaFileName = "custom-meta.json"

----<dataset-id>/ --------custom-meta.json - Custom metadata for this dataset, usually to set dataset title, but can also contain matched image scale/bias or other fields

const DatasetCustomRoot = "dataset-addons"

- dataset-addons/

const DatasetFileName = "dataset.bin"

----<dataset-id>/ --------dataset.bin - The dataset file containing all spectra, housekeeping, beam locations, etc. Created by data-converter

const DatasetLastImportTimesPath = RootDatasetConfig + "/import-times.json"

----import-times.json - Specifies when each dataset was imported (map id->unix time)

const DatasetSummaryFileName = "summary.json"

--------summary.json - Contains metadata for the dataset, easily downloadable/browsable. dataset-tile-updater pulls these in to form the datasets.json file

const DatasetUploadRoot = "UploadedDatasets"

Users can upload datasets here: - Uploaded/

const DiffractionDBFileName = "diffraction-db.bin"

--------diffraction-db.bin - Diffraction peak database, generated by diffraction-detector when dataset is imported

const DiffractionPeakManualFileName = "manual-diffraction-peaks.json"

----shared/ - Same as for a <user-id> but contains all files that were shared. These are copies of the user ones, along with " ---- NOTE: Special case is diffraction/roughness user files, these only exist in shared directory

const DiffractionPeakStatusFileName = "diffraction-peak-statuses.json"

const ExpressionExecutionStatPath = "ExpressionExecStat"

const ExpressionFile = "DataExpressions.json"

--------DataExpressions.json - User created expressions

const JobStatusSuffix = "-status.json"

----<dataset-id>/<job-id>-status.json

const JobSummarySuffix = "-jobs.json"

----<dataset-id>-jobs.json - Summary files describing all jobs for a dataset

const MultiQuantZStackFile = "multi-quant-z-stack.json"

multi-quant-z-stack.json - The current z-stack on multi-quant panel

const PiquantConfigFileName = "config.json"

const PiquantConfigSubDir = "PiquantConfigs" // - NOTE: Quant creation doesn't use GetDetectorConfigPath, maybe DetectorConfig is hard-coded into docker container!

----<config-name>/ - Name shown on UI, eg PIXL or Breadboard --------pixlise-config.json - UI config values for this detector, eg detector energy range, window material, etc --------PiquantConfigs/

const PiquantDownloadPath = "piquant"

- piquant/ ----piquant-linux-*.zip - Built PIQUANT executables (zipped)

const PiquantLogSubdir = "piquant-logs"

----<dataset-id>/ --------<job-id>/ ------------node*.pmcs - PMC list for a given node running the job ------------params.json - Job parameters as specified when created ------------output/ ----------------node*.pmcs_result.csv - CSV generated by a single node, intermediate outpu ----------------combined.csv - The final output generated by combining all the node*.pmcs_result.csv files ------------piquant-logs/

const PiquantVersionFileName = "piquant-version.json"

----piquant-version.json - Config contains the docker container to use for PIQUANT. Separate from config.json because users can configure this in UI

const QuantFileSuffix = ".bin"

QuantFileSuffix - quant files are <jobid>.bin

const QuantLastOutputFileName = "output_data" // Extension added as needed

const QuantLastOutputLogName = "output.log"

const QuantLogsSubDirSuffix = "-logs"

QuantLogsSubDirSuffix - this goes after job ID to form a directory name that stores the quant logs

const QuantSummaryFilePrefix = "summary-"

QuantSummaryFilePrefix - summary files are summary-<jobid>.json

const RootArchive = "Archive"

- Archive/

const RootDatasetConfig = "DatasetConfig"

- DatasetConfig/

const RootDatasetSummaries = "DatasetSummaries" // Where we put all dataset summary files, named <datset-id>.json

- DatasetSummaries/

const RootDatasets = "Datasets"

- Datasets/

const RootDetectorConfig = "DetectorConfig"

- DetectorConfig/

const RootJobData = "JobData"

This contains temporary files generated when running a long-running job (eg PIQUANT). Contains parameters to the job, status files, log files from the job, intermediate calculation files These are in separate directories to aid listing, so instead of returning 100s of files per job you may only want a list of job statuses, where you'd only get 1 file per job Contains: - JobData/

const RootJobStatus = "JobStatus"

- JobStatus/

const RootJobSummaries = "JobSummaries"

- JobSummaries/

const RootPixliseConfigPath = "PixliseConfig"

- PixliseConfig/

const RootUserActivity = "Activity"

- Activity/

const RootUserContent = "UserContent"

- UserContent/

const ViewStateCollectionsSubpath = "WorkspaceCollections"

--------------------<workspace-name>.json - View state files (like up one directory) flattened to a file and given a workspace name. Note the file also contains the workspace name, the file name may have been modified for saving, eg removal of / -------------------- See: GetWorkspacePath() -------------------- WorkspaceCollections/

const ViewStateSavedSubpath = "Workspaces"

----------------quantification.json - The quantification loaded on UI top toolbar ----------------roi.json - Colours assigned to ROIs on the UI ----------------selection.json - The users current selection of PMCs and/or pixels on UI ----------------analysisLayout.json - What widgets go where, top row/bottom row -----------------<panel-type>-<location>.json - States of various UI panels and where they are ----------------- See: GetViewStatePath() ----------------- Workspaces/

Functions

func GetAnnotationsPath

func GetAnnotationsPath(userID string, datasetID string) string

func GetCollectionPath

func GetCollectionPath(userID string, datasetID string, id string) string

func GetConfigFilePath

func GetConfigFilePath(fileName string) string

func GetCustomImagePath

func GetCustomImagePath(datasetID string, imgType string, fileName string) string

func GetCustomMetaPath

func GetCustomMetaPath(datasetID string) string

------------UNALINED/ ----------------image, *.png or *.jpg ------------MATCHED/ ----------------image, *.png, *.jpg or *.tif (if TIF it's considered an RGBU multi-spectral image) ------------RGBU/ ----------------images, *.tif - NOTE: Went unused, these are now all stored as MATCHED images

func GetDatasetFilePath

func GetDatasetFilePath(datasetID string, fileName string) string

--------Context image files (.png or .jpg) --------RGBU multi-spectral files (.tif)

func GetDatasetListPath

func GetDatasetListPath() string

----datasets.json - Dataset list (tiles). Regenerated every time Datasets/ changes by lambda function: dataset-tile-updater

func GetDatasetSummaryFilePath

func GetDatasetSummaryFilePath(datasetID string) string

func GetDatasetUploadPath

func GetDatasetUploadPath(datasetID string, fileName string) string

func GetDetectorConfigFilePath

func GetDetectorConfigFilePath(configName string) string

------------<version>/ - eg v1, v2, v3 ----------------config.json - The PIQUANT config file, used by quant "runner", in docker container. References other files

----------------<other files>.msa or .csv - These are referenced by config.json and passed to PIQUANT exe as parameters

func GetDetectorConfigPath

func GetDetectorConfigPath(configName string, version string, fileName string) string

func GetElementSetPath

func GetElementSetPath(userID string) string

func GetExpressionExecutionStatPath

func GetExpressionExecutionStatPath(exprID string) string

func GetExpressionPath

func GetExpressionPath(userID string) string

func GetJobDataPath

func GetJobDataPath(datasetID string, jobID string, fileName string) string

----------------node*.pmcs_piquant.log - PIQUANT log file for a given node ----------------node*.pmcs_stdout.log - stdout for running PIQUANT on a given node

func GetJobStatusPath

func GetJobStatusPath(datasetID string, jobID string) string

func GetJobSummaryPath

func GetJobSummaryPath(datasetID string) string

func GetMultiQuantZStackPath

func GetMultiQuantZStackPath(userID string, datasetID string) string

func GetRGBMixPath

func GetRGBMixPath(userID string) string

func GetROIPath

func GetROIPath(userID string, datasetID string) string

func GetSharedContentDatasetPath

func GetSharedContentDatasetPath(datasetID string, fileName string) string

func GetSharedQuantPath

func GetSharedQuantPath(datasetID string, fileName string) string

func GetTagPath

func GetTagPath(userID string) string

func GetUserContentDatasetPath

func GetUserContentDatasetPath(userID string, datasetID string, fileName string) string

func GetUserContentPath

func GetUserContentPath(userID string, fileName string) string

--------------------<collection-name>.json -------------------- See: GetCollectionPath()

The above paths can be created with the above file names...

func GetUserLastPiquantOutputPath

func GetUserLastPiquantOutputPath(userID string, datasetID string, piquantCommand string, fileName string) string

------------Path for last outputs, eg last run fit command (command is actually "quant"), sits in here with its log file

func GetUserQuantPath

func GetUserQuantPath(userID string, datasetID string, fileName string) string

----------------<quant-id>.bin - The combined.csv file converted to protobuf binary format by quant-converter ----------------<quant-id>.csv - Copied from Job Bucket/JobData/<job-id>/output/combined.csv ----------------<quant-id>-logs/ - Copied from Job Bucket/JobData/<job-id>/piquant-logs/ ----------------summary-<quant-id>.json - Quant summary file

func GetViewStatePath

func GetViewStatePath(userID string, datasetID string, fileName string) string

func GetWorkspacePath

func GetWorkspacePath(userID string, datasetID string, id string) string

func MakeQuantCSVFileName

func MakeQuantCSVFileName(quantID string) string

func MakeQuantDataFileName

func MakeQuantDataFileName(quantID string) string

func MakeQuantLogDirName

func MakeQuantLogDirName(quantID string) string

func MakeQuantSummaryFileName

func MakeQuantSummaryFileName(quantID string) string

MakeQuantSummaryFileName - Given a quant ID, generates the file name: summary-<jobid>.json (use this for searchability/consistency)