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LoadEventNexus v1¶
![../_images/LoadEventNexus-v1_dlg.png](../_images/LoadEventNexus-v1_dlg.png)
LoadEventNexus dialog.¶
Summary¶
Loads an Event NeXus file and stores as an EventWorkspace. Optionally, you can filter out events falling outside a range of times-of-flight and/or a time interval.
See Also¶
Properties¶
Name |
Direction |
Type |
Default |
Description |
---|---|---|---|---|
Filename |
Input |
string |
Mandatory |
The name of the Event NeXus file to read, including its full or relative path. The file name is typically of the form INST_####_event.nxs (N.B. case sensitive if running on Linux). Allowed extensions: [‘.nxs.h5’, ‘.nxs’, ‘_event.nxs’] |
OutputWorkspace |
Output |
Mandatory |
The name of the output EventWorkspace or WorkspaceGroup in which to load the EventNexus file. |
|
NXentryName |
Input |
string |
Optional: Name of the NXentry to load if it’s not the default. |
|
FilterByTofMin |
Input |
number |
Optional |
Optional: To exclude events that do not fall within a range of times-of-flight. This is the minimum accepted value in microseconds. Keep blank to load all events. |
FilterByTofMax |
Input |
number |
Optional |
Optional: To exclude events that do not fall within a range of times-of-flight. This is the maximum accepted value in microseconds. Keep blank to load all events. |
FilterByTimeStart |
Input |
number |
Optional |
Optional: To only include events after the provided start time, in seconds (relative to the start of the run). |
FilterByTimeStop |
Input |
number |
Optional |
Optional: To only include events before the provided stop time, in seconds (relative to the start of the run). |
BankName |
Input |
str list |
Optional: To only include events from one bank. Any bank whose name does not match the given string will have no events. |
|
SingleBankPixelsOnly |
Input |
boolean |
True |
Optional: Only applies if you specified a single bank to load with BankName. Only pixels in the specified bank will be created if true; all of the instrument’s pixels will be created otherwise. |
Precount |
Input |
boolean |
True |
Pre-count the number of events in each pixel before allocating memory (optional, default True). This can significantly reduce memory use and memory fragmentation; it may also speed up loading. |
CompressTolerance |
Input |
number |
-1 |
Run CompressEvents while loading (optional, leave blank or negative to not do). This specified the tolerance to use (in microseconds) when compressing. |
ChunkNumber |
Input |
number |
Optional |
If loading the file by sections (‘chunks’), this is the section number of this execution of the algorithm. |
TotalChunks |
Input |
number |
Optional |
If loading the file by sections (‘chunks’), this is the total number of sections. |
LoadMonitors |
Input |
boolean |
False |
Load the monitors from the file (optional, default False). |
MonitorsLoadOnly |
Input |
string |
If multiple repesentations exist, which one to load. Default is to load the one that is present. Allowed values: [‘’, ‘Events’, ‘Histogram’] |
|
FilterMonByTofMin |
Input |
number |
Optional |
Optional: To exclude events from monitors that do not fall within a range of times-of-flight. This is the minimum accepted value in microseconds. |
FilterMonByTofMax |
Input |
number |
Optional |
Optional: To exclude events from monitors that do not fall within a range of times-of-flight. This is the maximum accepted value in microseconds. |
FilterMonByTimeStart |
Input |
number |
Optional |
Optional: To only include events from monitors after the provided start time, in seconds (relative to the start of the run). |
FilterMonByTimeStop |
Input |
number |
Optional |
Optional: To only include events from monitors before the provided stop time, in seconds (relative to the start of the run). |
SpectrumMin |
Input |
number |
Optional |
The number of the first spectrum to read. |
SpectrumMax |
Input |
number |
Optional |
The number of the last spectrum to read. |
SpectrumList |
Input |
int list |
A comma-separated list of individual spectra to read. |
|
MetaDataOnly |
Input |
boolean |
False |
If true, only the meta data and sample logs will be loaded. |
LoadLogs |
Input |
boolean |
True |
Load only the Sample/DAS logs from the file (default True). |
LoadAllLogs |
Input |
boolean |
False |
Load all the logs from the nxs, without checking or processing them; if checked, LoadLogs will be ignored; use with caution |
LoadType |
Input |
string |
Default |
Set type of loader. 2 options {Default, Multiproceess},’Multiprocess’ should work faster for big files and it is experimental, available only in Linux. Allowed values: [‘Default’, ‘Multiprocess (experimental)’] |
LoadNexusInstrumentXML |
Input |
boolean |
True |
Reads the embedded Instrument XML from the NeXus file (optional, default True). |
NumberOfBins |
Input |
number |
500 |
The number of bins intially defined. Use Rebin to change the binning later. If there is no data loaded, or you select meta data only you will only get 1 bin. |
AllowList |
Input |
str list |
If specified, only these logs will be loaded from the file (each separated by a space). |
|
BlockList |
Input |
str list |
If specified, these logs will NOT be loaded from the file (each separated by a space). |
Description¶
The LoadEventNeXus algorithm loads data from an EventNexus file into an EventWorkspace. The histogram bin boundaries depend on the setting of NumberOfBins, which by default will be the whole range of time of flight able to hold all events (in all pixels) split into NumberOfBins linear bins, and will have their units set to time-of-flight. Since it is an EventWorkspace, it can be rebinned to finer bins with no loss of data.
Child algorithms used¶
Sample logs, such as motor positions or e.g. temperature vs time, are also loaded using LoadNexusLogs.
Monitors are loaded using LoadNexusMonitors.
Instrument geometry
There are a series of approaches for extracting the instrument geometry. These follow the escalation path as follows:
Tries to load embedded instrument_xml from the NXinstrument if present using LoadIDFFromNexus.
Else tries to load embedded nexus geometry from the NXinstrument if present
Else tries to load the instrument using the name extracted from NXinstrument
The latter two possibilities are achieved via LoadInstrument
Optional properties¶
If desired, you can filter out the events at the time of loading, by specifying minimum and maximum time-of-flight values. This can speed up loading and reduce memory requirements if you are only interested in a narrow range of the times-of-flight of your data.
You can specify to load only certain spectra within the file, using the SpectraMax, SpectraMin and SpectraList properties. This will load data only matching those restrictions. At facilities that do not group detectors in hardware such as the SNS, then this will also equate to the detector IDs.
You may also filter out events by providing the start and stop times, in seconds, relative to the first pulse (the start of the run).
If you wish to load only a single bank, you may enter its name and no events from other banks will be loaded.
The Precount option will count the number of events in each pixel before allocating the memory for each event list. Without this option, because of the way vectors grow and are re-allocated, it is possible for up to 2x too much memory to be allocated for a given event list, meaning that your EventWorkspace may occupy nearly twice as much memory as needed. The pre-counting step takes some time but that is normally compensated by the speed-up in avoid re-allocating, so the net result is smaller memory footprint and approximately the same loading time.
Veto Pulses¶
Veto pulses can be filtered out in a separate step using FilterByLogValue v1:
FilterByLogValue(InputWorkspace="ws", OutputWorkspace="ws", LogName="veto_pulse_time", PulseFilter="1")
Data Loaded from Nexus File¶
If LoadAllLogs is checked, all the logs in the Nexus files will be loaded directly in the sample logs as they are. The LoadLogs flag will be ignored. If only LoadLogs is checked, only a subset of the logs will be processed and loaded, in the manner described afterward.
The nexus file must have /raw_data_1
or /entry
as its main group and
that group be of type NXentry
. It also needs a group of type NXevent_data
.
The data is read from each group of type NXevent_data
.
If the file has an isis_vms_compat
then it is taken to be an ISIS file and
the data will be modified according to the information obtained from this group.
Here are some tables that show it in more detail:
Description of Data |
Found in Nexus file (within ‘raw_data_1’) |
Placed in Workspace (Workspace2D) |
---|---|---|
Monitor Data |
groups of Class NXMonitor (one monitor per group) |
Monitor Data |
Detector Data |
groups of Class NXevent_data (one bank per group) |
Event data |
Instrument |
group |
Workspace instrument if not overridden |
Spectrum of each detector ID |
If |
Spectra-Detector mapping |
Run |
mainly as loaded from LoadNexusLogs v1 |
Run Object |
Sample |
If |
Sample Object |
Invalid Period Logs Error¶
There is an issue specific to ISIS, particularly on long runs, where noise on data collection instruments can change the period of the data. This can cause the period associated with certain data points to exceed the total number of periods we expect.
LoadEventNeXus compares the total number of periods we expect, which can be found in the periods/number attribute of the run, and the greatest period number found in framelog/period_log/value attribute of the data. If they do not match, an error message is raised which explains this problem, and loading of the data will be unsuccessful.
In this case, the data is fundamentally corrupted, so Mantid does not know how to correct this automatically. If you only expect 1 period, there is a script in the script repository, user/TomTitcombe/correct_period_logs.py, which will change all the periods in framelog/period_log/value to 1.
If you expect more than 1 periods, there is currently no solution script available through Mantid. You should contact the Mantid team to discuss the problem and possible solutions.
Sample Object¶
If isis_vms_compat
exists,
then the following sample properties are read from it:
Nexus |
Workspace sample object |
---|---|
|
Geometry flag |
|
Thickness |
|
Height |
|
Width |
This is the same as read by LoadISISNexus v2.
Usage¶
Note
To run these usage examples please first download the usage data, and add these to your path. In Mantid this is done using Manage User Directories.
Example - Load SNS/ISIS event Nexus file:
# Load SNS HYS event dataset
ws = LoadEventNexus('HYS_11092_event.nxs')
print("The number of histograms (spectra) is: {}".format(ws.getNumberHistograms()))
Output:
The number of histograms (spectra) is: 20480
Example - Load event nexus file with time filtering:
# Load SNS CNCS event dataset between 1 and 2 minutes
ws = LoadEventNexus('CNCS_7860_event.nxs', FilterByTimeStart=60, FilterByTimeStop=120)
print("The number of events: {}".format(ws.getNumberEvents()))
Output:
The number of events: 29753
Categories: AlgorithmIndex | DataHandling\Nexus
Source¶
C++ header: LoadEventNexus.h
C++ source: LoadEventNexus.cpp