------------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.

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

----datasets.json - Dataset list (tiles).

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

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

--------------------<collection-name>.json -------------------- See: GetCollectionPath() The above paths can be created with the above file names...

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

----------------<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.

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

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

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

CSVFileSuffix - CSV files are <jobid>.csv.

----<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.

- dataset-addons/.

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

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

--------summary.json - Contains metadata for the dataset, easily downloadable/browsable.

Users can upload datasets here: - Uploaded/.

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

----shared/ - Same as for a <user-id> but contains all files that were shared.

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

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

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

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

- NOTE: Quant creation doesn't use GetDetectorConfigPath, maybe DetectorConfig is hard-coded into docker container!.

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

----<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/.

----piquant-version.json - Config contains the docker container to use for PIQUANT.

QuantFileSuffix - quant files are <jobid>.bin.

Extension added as needed.

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

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

- Archive/.

- DatasetConfig/.

- Datasets/.

Where we put all dataset summary files, named <datset-id>.json.

- DetectorConfig/.

This contains temporary files generated when running a long-running job (eg PIQUANT).

- JobStatus/.

- JobSummaries/.

- PixliseConfig/.

- Activity/.

- UserContent/.

--------------------<workspace-name>.json - View state files (like up one directory) flattened to a file and given a workspace name.

----------------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/.