pIMZ Modules¶
imzML Parser¶
a imzML
SpectraRegion¶
a SpectraRegion
Clustering Module¶
a Clustering
Comparative¶
a Comparative
HuBMap Downloader¶
a downloader
- class pIMZ.hubmap_downloader.HuBMAPDownloader¶
The HuBMAPDownloader let’s the user download whole experiment folders from the public HuBMAP release on globus.
A globus account is required to sign in.
The user has to enter an endpoint to where the data is transferred. On a local machine, this most probably required globus connect personal.
- cancel_transfer(transferID)¶
Cancels the data transfer with transferID
- Parameters
transferID (str) – Transfer ID to cancel.
- create_timestamp(deltaH=2)¶
Creates an ISO 8601 timestamp to set a deadline for globus
- Parameters
deltaH (int, optional) – The timestamp is calculated as now+deltaH (in hours).. Defaults to 2.
- Returns
UTC timestamp in ISO8601 format
- Return type
str
- get_local_endpoint()¶
Fetches the local endpoint. Returns None if no local endpoint is available.
Ensure that your globus connect personal is running!
- Returns
local endpoint id
- Return type
str
- list_my_endpoints()¶
Lists all user endpoints
- transfer_experiment(experiment_data_id, local_path, label=None, local_endpoint_id=None, give_hours=2)¶
Transfers an experiment from HuBMAP to the local_endpoint_id in the path local_path
- Parameters
experiment_data_id (str) – Experiment ID as given by HuBMAP (this usually is the global folder name)
local_path (str) – Path in local endpoint where to store data
label (str, optional) – Name of the data transfer. Defaults to experiment_data_id.
local_endpoint_id (str, optional) – Target endpoint id. Defaults to None.
give_hours (int, optional) – Timelimit for transfer. This will set the deadline in the datatransfer. Defaults to 2.
- Returns
transfer id of started transfer
- Return type
[str]
- transfer_states()¶
Lists all transfer states of transfers started via this interface (also completed ones).