cheetah
Cheetah
This module contains Cheetah, a data-processing program for Serial X-ray Crystallography, based on OM but not designed to be run in real time.
CheetahProcessing
Bases: OmProcessingProtocol
See documentation for the __init__ function.
__init__(*, monitor_parameters)
Cheetah.
This Processing class implements the Cheetah software package. Cheetah processes detector data frames, detecting Bragg peaks in each frame using the Peakfinder8PeakDetection algorithm. It retrieves information about the location, size, intensity, SNR and maximum pixel value of each peak, Cheetah then saves the calibrated and corrected detector data, plus all the information retrieved from the facility or extracted from the data, in multi-event HDF5 files. Cheetah can also compute, and write to HDF5 sum files, sums of detector data frames (calculating separate sums for hit and non-hit frames). The sums can saved together with their corresponding Virtual Powder patterns.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
monitor_parameters |
MonitorParameters
|
An object storing OM's configuration parameters. |
required |
initialize_processing_node(*, node_rank, node_pool_size)
Initializes the processing nodes for Cheetah.
This function initializes all the required algorithms (peak finding, binning, etc.), plus some internal counters.
Please see the documentation of the base Protocol class for additional information about this method.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
node_rank |
int
|
The OM rank of the current node, which is an integer that unambiguously identifies the current node in the OM node pool. |
required |
node_pool_size |
int
|
The total number of nodes in the OM pool, including all the processing nodes and the collecting node. |
required |
initialize_collecting_node(node_rank, node_pool_size)
Initializes the collecting node for Cheetah.
This function initializes the data accumulation algorithms, the storage buffers used to compute statistics on the detected Bragg peaks and all the file writers.
Please see the documentation of the base Protocol class for additional information about this method.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
node_rank |
int
|
The OM rank of the current node, which is an integer that unambiguously identifies the current node in the OM node pool. |
required |
node_pool_size |
int
|
The total number of nodes in the OM pool, including all the processing nodes and the collecting node. |
required |
process_data(*, node_rank, node_pool_size, data)
Processes a detector data frame and saves the extracted data to HDF5 file.
This function processes retrieved data events, extracting the Bragg peak information. It also saves the frame-related processed data in an output HDF5 file, if a frame is identified as a hit. Finally, it prepares the reduced data (and optionally, the detector frame data) for transmission to the collecting node.
Please see the documentation of the base Protocol class for additional information about this method.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
node_rank |
int
|
The OM rank of the current node, which is an integer that unambiguously identifies the current node in the OM node pool. |
required |
node_pool_size |
int
|
The total number of nodes in the OM pool, including all the processing nodes and the collecting node. |
required |
data |
Dict[str, Any]
|
A dictionary containing the data that OM retrieved for the detector data frame being processed.
|
required |
Returns:
| Type | Description |
|---|---|
Tuple[Dict[str, Any], int]
|
A tuple with two entries. The first entry is a dictionary storing the processed data that should be sent to the collecting node. The second entry is the OM rank number of the node that processed the information. |
wait_for_data(*, node_rank, node_pool_size)
Receives and handles requests from external programs.
This function is not used in Cheetah, and therefore does nothing.
Please see the documentation of the base Protocol class for additional information about this method.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
node_rank |
int
|
The OM rank of the current node, which is an integer that unambiguously identifies the current node in the OM node pool. |
required |
node_pool_size |
int
|
The total number of nodes in the OM pool, including all the processing nodes and the collecting node. |
required |
collect_data(*, node_rank, node_pool_size, processed_data)
Computes statistics on aggregated data and saves them to files.
This function collects and accumulates frame- and peak-related information received from the processing nodes. Optionally, it computes the sums of hit and non-hit detector frames and the corresponding virtual powder patterns, and saves them to file. Additionally, this function writes information about the processing statistics (number of processed events, number of found hits and the elapsed time) to a status file at regular intervals. External programs can inspect the file to determine the advancement of the data processing.
Please see the documentation of the base Protocol class for additional information about this method.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
node_rank |
int
|
The OM rank of the current node, which is an integer that unambiguously identifies the current node in the OM node pool. |
required |
node_pool_size |
int
|
The total number of nodes in the OM pool, including all the processing nodes and the collecting node. |
required |
processed_data |
Tuple[Dict, int]
|
A tuple whose first entry is a dictionary storing the data received from a processing node, and whose second entry is the OM rank number of the node that processed the information. |
required |
end_processing_on_processing_node(*, node_rank, node_pool_size)
Ends processing on the processing nodes for Cheetah.
This function prints a message on the console, closes the output HDF5 files and ends the processing.
Please see the documentation of the base Protocol class for additional information about this method.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
node_rank |
int
|
The OM rank of the current node, which is an integer that unambiguously identifies the current node in the OM node pool. |
required |
node_pool_size |
int
|
The total number of nodes in the OM pool, including all the processing nodes and the collecting node. |
required |
Returns:
| Type | Description |
|---|---|
Union[Dict[str, Any], None]
|
Usually nothing. Optionally, a dictionary storing information to be sent to the processing node. |
end_processing_on_collecting_node(*, node_rank, node_pool_size)
Ends processing on the collecting node for Cheetah.
This function prints a message on the console, writes the final information in the sum and status files, closes the files and ends the processing.
Please see the documentation of the base Protocol class for additional information about this method.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
node_rank |
int
|
The OM rank of the current node, which is an integer that unambiguously identifies the current node in the OM node pool. |
required |
node_pool_size |
int
|
The total number of nodes in the OM pool, including all the processing nodes and the collecting node. |
required |