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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 GetDetectorConfigFilePath(configName string) string
- func GetDetectorConfigPath(configName string, version string, fileName string) string
- func GetElementSetPath(userID 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 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 APIConfigFileName = "config.json"
config.json - API config file it downloads on startup, contains buckets, keys, kubernetes settings, etc
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 DatasetFileName = "dataset.bin"
<dataset-id>/
dataset.bin - The dataset file containing all spectra, housekeeping, beam locations, etc. Created by data-converter
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 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 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"
////////////////////////////////////////////////////////////////////////////////// Artifacts Built Bucket - where we go to download built PIQUANT, etc //////////////////////////////////////////////////////////////////////////////////
- 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 RootDatasets = "Datasets"
- Datasets/
const RootDetectorConfig = "DetectorConfig"
- DetectorConfig/
const RootJobData = "JobData"
////////////////////////////////////////////////////////////////////////////////// Job Bucket ////////////////////////////////////////////////////////////////////////////////// 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 RootUserContent = "UserContent"
////////////////////////////////////////////////////////////////////////////////// User Content Bucket ////////////////////////////////////////////////////////////////////////////////// - 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/
Variables ¶
This section is empty.
Functions ¶
func GetAnnotationsPath ¶
func GetConfigFilePath ¶
func GetCustomImagePath ¶
func GetCustomMetaPath ¶
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 ¶
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 GetDetectorConfigFilePath ¶
<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 GetElementSetPath ¶
func GetExpressionPath ¶
func GetJobDataPath ¶
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 GetJobSummaryPath ¶
func GetMultiQuantZStackPath ¶
func GetRGBMixPath ¶
func GetROIPath ¶
func GetSharedQuantPath ¶
func GetUserContentPath ¶
<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 ¶
<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 MakeQuantCSVFileName ¶
func MakeQuantDataFileName ¶
func MakeQuantLogDirName ¶
func MakeQuantSummaryFileName ¶
MakeQuantSummaryFileName - Given a quant ID, generates the file name: summary-<jobid>.json (use this for searchability/consistency)
Types ¶
This section is empty.
Source Files