Tomography tasks#
How to use
These tasks come from tomwer. It can be installed with
pip install tomwer
ℹ️ These tasks are used at the following ESRF beamlines: BM05, ID11, ID16B, ID17, BM18, ID19
FutureSupervisorTask#
Task used to wait for a 'FutureTomwerObject' and convert it to original instance of:
* TomwerScanBase (data): if the FutureTomwerObject is based on a scan instance
* TomwerVolumeBase (volume): if the FutureTomwerObject is based on a volume instance
* tuple of IcatReconstructedVolumeDataset (data_portal_processed_datasets): if the FutureTomwerObject is based on a volume instance
- Identifier:
tomwer.core.process.cluster.supervisor.FutureSupervisorTask- Task type:
class
- Required inputs:
future_tomo_obj
- Optional inputs:
- Outputs:
volume, data, data_portal_processed_datasets
FileNameFilterTask#
Task to filter a scan according to his name and a 'unix file name pattern' or a 'regular expression'
- Identifier:
tomwer.core.process.conditions.filters.FileNameFilterTask- Task type:
class
- Required inputs:
data, pattern
- Optional inputs:
serialize_output_data
- Outputs:
data
FileNameFilter#
- Identifier:
tomwer.core.process.conditions.filters.FileNameFilter- Task type:
class
- Required inputs:
data, pattern
- Optional inputs:
serialize_output_data
- Outputs:
data
DataWatcherEwoksTask#
For now the data watcher is a 'special case'. Because it will trigger downstream workflows / prcessing each time it discover
a new scan.
To move to 'default' ewoks workflows. Like launching it from the command line the simpler for now is to
simply pass the `data` input that user can fill manually.
- Identifier:
tomwer.core.process.control.datawatcher.datawatcher.DataWatcherEwoksTask- Task type:
class
- Required inputs:
data
- Optional inputs:
- Outputs:
data
TomoEmailTask#
Dedicated task for tomography and gui approach
- Identifier:
tomwer.core.process.control.emailnotifier.TomoEmailTask- Task type:
class
- Required inputs:
configuration, tomo_obj
- Optional inputs:
- Outputs:
tomo_obj
ConcatenateNXtomoTask#
Task used to concatenate a list of NXtomo (NXtomoScan) into a single NXtomo
- Identifier:
tomwer.core.process.control.nxtomoconcatenate.ConcatenateNXtomoTask- Task type:
class
- Required inputs:
output_file, series, output_entry, overwrite
- Optional inputs:
serialize_output_data, progress
- Outputs:
data
H5ToNxProcess#
Task to convert from a bliss dataset to a nexus compliant dataset
- Identifier:
tomwer.core.process.control.nxtomomill.H5ToNxProcess- Task type:
class
- Required inputs:
h5_to_nx_configuration
- Optional inputs:
bliss_scan, serialize_output_data, progress
- Outputs:
series, data
EDFToNxProcess#
Task calling edf2nx in order to insure conversion from .edf to .nx (create one NXtomo to be used elsewhere)
- Identifier:
tomwer.core.process.control.nxtomomill.EDFToNxProcess- Task type:
class
- Required inputs:
edf_to_nx_configuration
- Optional inputs:
edf_scan, serialize_output_data, progress
- Outputs:
data
SingleTomoObjProcess#
For now data can only be a single element and not a list. This must be looked at. Also when part of an ewoks graph ‘data’ is mandatory which is not the class when part of a orange workflow. Those can be added interactively
- Identifier:
tomwer.core.process.control.singletomoobj.SingleTomoObjProcess- Task type:
class
- Required inputs:
- Optional inputs:
tomo_obj
- Outputs:
tomo_obj
TimerTask#
Simple timer / time out - function
- Identifier:
tomwer.core.process.control.timer.TimerTask- Task type:
class
- Required inputs:
data, wait
- Optional inputs:
serialize_output_data
- Outputs:
data
Timer#
- Identifier:
tomwer.core.process.control.timer.Timer- Task type:
class
- Required inputs:
data, wait
- Optional inputs:
serialize_output_data
- Outputs:
data
PublishICatDatasetTask#
publish a list of 'IcatDataBase' instances.
`IcatDataBase` provide API to retrieve data and metadata to be publish
input field:
* data_portal_processed_datasets: list of 'DracDatasetBase' instances.
* beamline: name of the beamline (bm05, id19...)
* proposal: proposal name
- Identifier:
tomwer.core.process.drac.publish.PublishICatDatasetTask- Task type:
class
- Required inputs:
beamline, dataset, data_portal_processed_datasets, proposal
- Optional inputs:
process, dry_run
- Outputs:
DarkFlatPatchTask#
Patch an existing NXtomo calling nxtomomill
- Identifier:
tomwer.core.process.edit.darkflatpatch.DarkFlatPatchTask- Task type:
class
- Required inputs:
configuration, data
- Optional inputs:
serialize_output_data
- Outputs:
data
DarkFlatPatch#
- Identifier:
tomwer.core.process.edit.darkflatpatch.DarkFlatPatch- Task type:
class
- Required inputs:
configuration, data
- Optional inputs:
serialize_output_data
- Outputs:
data
ImageKeyEditorTask#
task to edit `image_key` field of a NXtomo ('data' input)
- Identifier:
tomwer.core.process.edit.imagekeyeditor.ImageKeyEditorTask- Task type:
class
- Required inputs:
configuration, data
- Optional inputs:
serialize_output_data
- Outputs:
data
ImageKeyUpgraderTask#
close to ImageKeyEditor but convert a full "family" of frame type to another
like all projections to dark field
- Identifier:
tomwer.core.process.edit.imagekeyeditor.ImageKeyUpgraderTask- Task type:
class
- Required inputs:
operations, data
- Optional inputs:
serialize_output_data
- Outputs:
data
ImageKeyUpgrader#
- Identifier:
tomwer.core.process.edit.imagekeyeditor.ImageKeyUpgrader- Task type:
class
- Required inputs:
operations, data
- Optional inputs:
serialize_output_data
- Outputs:
data
NXtomoEditorTask#
task to edit a couple of field of a NXtomo
- Identifier:
tomwer.core.process.edit.nxtomoeditor.NXtomoEditorTask- Task type:
class
- Required inputs:
configuration, data
- Optional inputs:
- Outputs:
data
SinoNormalizationTask#
Task to define the normalization to apply to a sinogram before reconstructing it with nabu
- Identifier:
tomwer.core.process.reconstruction.normalization.normalization.SinoNormalizationTask- Task type:
class
- Required inputs:
data
- Optional inputs:
serialize_output_data
- Outputs:
data
PythonScript#
- Identifier:
tomwer.core.process.script.python.PythonScript- Task type:
class
- Required inputs:
- Optional inputs:
volume, data, serialize_output_data
- Outputs:
volume, data