Utilities¶
h5tree¶
Description:¶
A function to output the data-tree from an hdf5 file object.
Args:¶
h5 (h5py.File) – Any H5File object, from h5py.
Returns:¶
None
Example Usage:¶
from sgmdata.utilities import h5tree
import h5py
f = h5py.File("Filename.nxs", 'r')
h5tree(f)
plot1d¶
Description:¶
Convenience function for plotting a bokeh lineplot, assumes Bokeh is already loaded.
Args:¶
xarr (array-like) – Independent array-like object, or list of array-like objects.
yarr (array-like) – Dependent array-like object, or list of array-like objects, same shape as xarr
title (str) – Plot title
labels (list(str)) – Legend labels for multiple objects, defaults to Curve0, Curve1, etc.
Returns:¶
None
preprocess¶
Description:¶
Utility for automating the interpolation and averaging of a sample in the SGMLive website.
Args:¶
sample (str): The name of the sample in your account that you wish to preprocess. or: data_id (int): The primary key of the dataset to preprocress.
Keywords:¶
All of the below are optional. proposal (str) – name of proposal to limit search to.
user (str) – name of user account to limit search to (for use by staff).
resolution (float) – to be passed to interpolation function, this is histogram bin width.
start (float) – start energy to be passed to interpolation function.
stop (float) – stop energy to be passed to interpolation function.
sdd_max (int) – threshold value to determine saturation in SDDs, to determine scan_health (default is 105000). bscan_thresh (tuple) – (continuous, dumped, and saturated) these are the threshold percentages from scan_health that will label a scan as ‘bad’. report (str) – Analysis report type, e.g. “XAS Report”. report_id (int) – primary key of report to be updated.
Returns:¶
SGMQuery object if query_return is True
Example Usage:¶
from sgmdata import preprocess
preprocess(sample="TiO2", user='regiert', resolution=0.1)
badscans¶
Description:¶
Batch calculation of sgmdata.utilities.scan_health for list of interpolated dataframes.
Args:¶
interp (list) : list of SGMScan binned dataframes.
Returns:¶
List of indexes for bad scans in interp.
predict_num_scans¶
Description:¶
Takes the SGMData object of a sample and uses a combination of other functions to predict how many additional scans should be taken of that sample.
Args:¶
data (type: SGMData object) – The SGMData object for the sample on which the user would like more information. verbose (type: optional boolean) – Default value is False. If set to True, gives user additional data on how the additional number of scans needed was calculated. percent_of_log (type: optional float) – Default value is 0.4. The average of the noise values of the first ten scans is taken, and the log of it is found. Scans continue to be taken, and the average of the noise values of the most recent ten scans is taken. The log of this average is taken,and if it’s less than percent_of_log multiplied by the log of the first ten averages, then scanning stops. num_scans (type: optional int) – Default value is 10. The number of scans from the scans provided by the user, that the user would like to be used to predict the number of additional scans to take.
Returns:¶
(int): The predicted number of additional scans that should be taken of a sample.
create_csv¶
Description:¶
Make CSV file from sample(s)
Args:¶
sample (str or list(str)) – Sample(s) name(s) from SGMLive that you want to process.
Keywords:¶
mcas (list(str)) – list of detector names for which the ROI summation should take place.
proposal (str) – SGMLive proposal name, will search all if none.
user (str) – SGMLive account name, defaults to current jupyterhub user.
out (os.path / str) – System path to output directory for csv file(s)
I0 (pandas.DataFrame)* – Dataframe including an incoming flux profile to be joined to the sample dataframe and included in the each CSV file.
ROI (tuple)* – Set the upper and lower bin number for the Region-of-Interest integration to be used in reducing the dimensionality of energy MCA data.
step (bool) – If the scans you’re interested in are step scans, then set True to bypass the imposed interpolation.
Returns:¶
list(pd.DataFrame) – list of dataframes created.
OneList¶
Description:¶
List extension that will return the sole item of the list if len(list) == 1
Usage:¶
data = {"key":1}
l = OneList([data])
assert l == data
print(l['key']) #prints 1
l.append(2)
print(l[1]) #prints 2
assert l == data #raises Error
DisplayDict¶
Description¶
dict class extension that includes repr_html for key,value display in Jupyter.