automatic import of python-reixs

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+/reixs-0.5.11.tar.gz
diff --git a/python-reixs.spec b/python-reixs.spec
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+%global _empty_manifest_terminate_build 0
+Name:		python-reixs
+Version:	0.5.11
+Release:	1
+Summary:	Library to analyse, plot, and export data taken at the REIXS Beamline at the Canadian Light Source, Saskatoon, Canada.
+License:	MIT License
+URL:		https://github.com/pmb399/REIXSAnalysis
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/1c/20/32f53f20ec66048f627ad0af395e8a560f4b6ba2bb76bf94d6edec37f157/reixs-0.5.11.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-numpy
+Requires:	python3-pandas
+Requires:	python3-bokeh
+Requires:	python3-scipy
+Requires:	python3-ipywidgets
+Requires:	python3-ipyfilechooser
+Requires:	python3-h5py
+
+%description
+# CLS REIXS Analysis
+
+This is a library to analyse, plot, and export REIXS beamline data. The package is meant to provide a framework to load data into jupyter and enable data interaction.
+
+Further [beamline information](https://reixs.lightsource.ca/) is available on the Website of the Canadian Light Source.
+
+## Installation
+
+Install the package from PyPi with the pip package manager. This is the recommended way to obtain a copy for your local machine and will install all required dependencies.
+
+```
+    $ pip install reixs
+```
+
+You will also need [Jupyter Notebook](https://github.com/jupyter) together with python 3 on your local machine.
+
+In case that certain widgets aren't rendered properly, make sure to enable the appropriate jupyter extensions
+
+```
+    $ jupyter nbextension enable --py widgetsnbextension
+```
+
+## Running
+
+Launch your local jupyter installation with
+
+```
+    $ jupyter notebook
+```
+
+## Examples
+
+### Load the required module
+
+Before you start, you will need to import the required reixs package, enable bokeh plotting, and set the base directory.
+
+```
+## Define base directory
+basedir = "/home/braun/ownCloud/Beamtime/example_data/"
+
+## Setup necessarry inputs
+from reixs.LoadData import *
+from bokeh.io import show, output_notebook
+output_notebook(hide_banner=True)
+```
+
+### 1d plots
+
+#### General Loader1d
+
+```
+sca = Load1d()
+sca.load(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4)  # Loads multiple scans individually
+sca.add(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4)  # Adds multiple scans
+sca.subtract(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4,norm=False) # Subtracts scans from the first scan
+sca.xlim(lower_lim,upper_lim) # Sets the horizontal axis plot region
+sca.ylim(lower_lim,upper_lim) # Sets the vertical axis plot region
+sca.plot_legend("pos string as per bokeh") # Determines a specific legend position
+sca.vline(position) # Draws a vertical line
+sca.hline(position) # Draws a horizontal line
+sca.label(pos_x,pos_y,'Text') # Adds a label to the plot
+sca.plot() # Plots the defined object
+sca.exporter() # Exports the data by calling an exporter widget
+```
+
+0. Create "Loader" object
+
+1. Specify the variable for the base directory (basedir)
+
+2. Enter the file name of the scan to analyse ('FileName.dat')
+
+3. Options for **x_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+- _MCP Energy_ (uncalibrated)
+- _SDD Energy_ (uncalibrated)
+- _XEOL Energy_ (uncalibrated, actually the wavelength scale)
+- _Points_ (by index)
+
+4. Options for **y_stream** quantities include:
+- All quantities in the header file
+- _TEY_ (Total Electron Yield: sample normalized by mesh)
+- _TFY_ (Total Fluorescence Yield, normalized by mesh)
+- _PFY_ and _iPFY_ (Partial Fluorescence Yield and Inverse Partial Fluorescence Yield, both normalized by mesh)
+  Specify ROI with brackets, either by XAS edge or energy:
+  e.g. _PFY[O]_ for PFY at the O K edge
+  e.g. _PFY[490:560]_ for PFY from 490eV to 560eV
+- _specPFY_ (spectrometer PFY, normalized by mesh)
+  specify energy range
+  e.g. specPFY[500:520]
+- _XES_ and _rXES_ (X-Ray emission and resonant x-ray emission at selected energies from the spectrometer MCP data)
+  e.g. rXES[560:565]
+- _XRF_ and _rXRF_ (X-Ray fluorescence and resonant x-ray fluorescence at selected energies from the SDD data)
+  e.g. rXRF[550:570]
+- _XEOL_ and _rXEOL_ (XEOL data from the optical spectrometer)
+- _POY_ and _TOY_ (Partial optical yield and total optical yield, normalized by mesh)
+  e.g. POY[300:750]
+- _EY_ or _Sample_ (Sample current, not normalized by mesh)
+- _Mesh_ (Mesh current)
+- _ET_ (Energy Transfer data, integrates over energy loss ROI and probes constant final states, sometimes referred to as CET scan)
+  specify energy transfer region
+  e.g. ET[-2:5] to probe mostly scattering close to the elastic line
+- _rLOSS_ (Resonantly excited emission data on energy loss scale, integrates over incident energy ROIS and probes constant intermediate states, sometimes referred to as CIE scan)
+  specify incident energy region
+  e.g. rLOSS[620:640]
+
+5. List all scans to analyse (comma-separated)
+
+6. Set optional flags. Options include:
+- _norm_ (Normalizes to [0,1])
+- _xcoffset_ (Defines a constant shift in the x-stream)
+- _xoffset_ (Takes a list of tuples and defines a polynomial fit of the x-stream)
+- _ycoffset_ (Defines a constant shift in the y-stream)
+- _yoffset_ (Takes a list of tuples and defines a polynomial fit of the y-stream)
+  e.g. offset = [(100,102),(110,112),(120,121)]
+- _background_ (Subtracts a XEOL background from XEOL scans)
+  Set to True, uses the getXEOLback function with the background data stored (only supported with HDF5)
+  Specify scan number, subtracts the XEOL scan taken at this particular scan
+- _energyloss_ (Transfers the resultant MCP scale to energy loss 
+  Set to True, then takes mean of mono energy array
+  Specify float with the incident photon energy
+- _grid_x_ (Takes a list with three arguments to apply 1d interpolation gridding)
+  e.g. grid_x = [Start Energy, Stop Energy, Delta]
+- _savgol_ (Takes a list with two or three arguments to apply data smoothing and derivatives)
+  e.g. savgol = [Window length, Polynomial order, deriavtive] as specified in the scipy Savitzky-Golay filter
+- _binsize_ (int, allows to perform data binning to improve Signal-to-Noise)
+- _legend_items_ (dict={scan_number:"name"}, overwrites generic legend names; works for the _load_ method)
+- _legend_item_ (str, overwrites generic legend name in the _add_/_subtract_ method)
+
+#### Absorption Scans
+
+```
+xas = XASLoader()
+xas.load(basedir,'Plate2a.dat','TEY',1,4,6)
+xas.load(basedir,'Plate2a.dat','PFY[O]',1,4)
+xas.add(basedir,'Plate2a.dat','PFY[500:520]',1,4)
+xas.subtract(basedir,'Plate2a.dat','specPFY[500:520]',1,4,6)
+xas.plot()
+xas.exporter()
+```
+
+#### Emission Scans (MCP)
+
+```
+xes = XESLoader()
+# Options: XES, rXES
+xes.load(basedir,'Plate2a.dat','XES',3,xoffset=[(515,520),(520,525),(530,535)])
+xes.load(basedir,'Plate2a.dat','rXES[520:560]',4)
+xes.add(basedir,'Plate2a.dat','XES',1,4)
+xes.subtract(basedir,'Plate2a.dat','XES',1,4)
+xes.plot()
+xes.exporter()
+```
+
+#### XRF Scans (SDD)
+
+```
+xrf = XRFLoader()
+# Options XRF,rXRF
+xrf.load(basedir,'Plate2a.dat','XRF',3)
+xrf.load(basedir,'Plate2a.dat','rXRF[520:560]',4)
+xrf.add(basedir,'Plate2a.dat','XRF',1,4,)
+xrf.subtract(basedir,'Plate2a.dat','XRF',1,4)
+xrf.plot()
+xrf.exporter()
+```
+
+#### XEOL Scans (Optical Spectrometer)
+
+```
+xeol = XEOLLoader()
+#Options: XEOL, rXEOL
+xeol.load(basedir,'RIXS_ES_QA.dat','XEOL',1,2,3,4,background=3)
+xeol.load(basedir,'RIXS_ES_QA.dat','XEOL',1,2,3,4,background=True)
+xeol.plot()
+```
+
+### 2d Images
+
+#### General loader for MCA detector data
+
+Note: Can only load one scan at a time!
+
+```
+load2d = Load2d()
+load2d.load(basedir,'Filename.dat','x_stream','y_stream','detector',1)
+load2d.plot()
+load2d.exporter()
+```
+
+0. Create "Loader" object
+
+1. Specify the variable for the base directory (basedir)
+
+2. Enter the file name of the scan to analyse ('FileName.dat')
+
+3. Options for **x_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+
+4. Options for **y_stream** quantities include:
+- _SDD Energy_ (Energy scale of the SDD detector)
+- _MCP Energy_ (Energy scale of the MCP detector)
+- _XEOL Energy_ (Wavelength scale of the XEOL optical spectrometer)
+
+5. Options for **detector** quantities include:
+- _SDD_ (SDD detector MCA)
+- _MCP_ (MCP detector MCA)
+- _XEOL_ (XEOL optical spectrometer MCA)
+
+6. List all scans to analyse (comma-separated)
+
+7. Set optional flags. Options include:
+- _norm_ (Normalizes to [0,1])
+- _xcoffset_ (Defines a constant shift in the x-stream)
+- _xoffset_ (Takes a list of tuples and defines a polynomial fit of the x-stream)
+- _ycoffset_ (Defines a constant shift in the y-stream)
+- _yoffset_ (Takes a list of tuples and defines a polynomial fit of the y-stream)
+  e.g. offset = [(100,102),(110,112),(120,121)]
+- _background_ (Subtracts a XEOL background from XEOL scans)
+  Set to True, uses the getXEOLback function with the background data stored (only supported with HDF5)
+  Specify scan number, subtracts the XEOL scan taken at this particular scan
+- _energyloss_ (Transfers the excitation-emission map to energy loss scale
+- _grid_x_ (Takes a list with three arguments to apply 1d interpolation gridding)
+  e.g. grid_x = [Start Energy, Stop Energy, Delta]
+
+#### EEMs (normalized by mesh current, special version of the general 2d image loader)
+
+Note: Can only load one scan at a time!
+
+```
+eems = EEMsLoader()
+eems.load(basedir,'Plate2a.dat','SDD',1)
+eems.load(basedir,'Plate2a.dat','MCP',1)
+eems.load(basedir,'RIXS_ES_QA.dat','XEOL',2,background=3)
+eems.plot()
+eems.exporter()
+```
+
+### Mesh Scans (Plots a 2d histogram)
+
+```
+mesh = LoadMesh()
+mesh.load(basedir,'Filename.txt','x_stream','y_stream','z_stream',24)
+mesh.plot()
+mesh.exporter()
+```
+
+0. Create "Loader" object
+
+1. Specify the variable for the base directory (basedir)
+
+2. Enter the file name of the scan to analyse ('FileName.dat')
+
+3. Options for **x_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+- _SDD Energy_ (Energy scale of the SDD detector)
+- _MCP Energy_ (Energy scale of the MCP detector)
+- _XEOL Energy_ (Wavelength scale of the XEOL optical spectrometer)
+
+4. Options for **y_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+- _SDD Energy_ (Energy scale of the SDD detector)
+- _MCP Energy_ (Energy scale of the MCP detector)
+- _XEOL Energy_ (Wavelength scale of the XEOL optical spectrometer)
+
+5. Options for **z_stream** quantities include:
+- All quantities in the header file
+- All special quantities as specified for the Load1d() function
+
+6. List all scans to analyse (comma-separated)
+
+7. Set optional flags. Options include:
+- _norm_ (Normalizes to [0,1])
+- _xcoffset_ (Defines a constant shift in the x-stream)
+- _xoffset_ (Takes a list of tuples and defines a polynomial fit of the x-stream)
+- _ycoffset_ (Defines a constant shift in the y-stream)
+- _yoffset_ (Takes a list of tuples and defines a polynomial fit of the y-stream)
+  e.g. offset = [(100,102),(110,112),(120,121)]
+- _background_ (Subtracts a XEOL background from XEOL scans)
+  Set to True, uses the getXEOLback function with the background data stored (only supported with HDF5)
+  Specify scan number, subtracts the XEOL scan taken at this particular scan
+
+
+%package -n python3-reixs
+Summary:	Library to analyse, plot, and export data taken at the REIXS Beamline at the Canadian Light Source, Saskatoon, Canada.
+Provides:	python-reixs
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-reixs
+# CLS REIXS Analysis
+
+This is a library to analyse, plot, and export REIXS beamline data. The package is meant to provide a framework to load data into jupyter and enable data interaction.
+
+Further [beamline information](https://reixs.lightsource.ca/) is available on the Website of the Canadian Light Source.
+
+## Installation
+
+Install the package from PyPi with the pip package manager. This is the recommended way to obtain a copy for your local machine and will install all required dependencies.
+
+```
+    $ pip install reixs
+```
+
+You will also need [Jupyter Notebook](https://github.com/jupyter) together with python 3 on your local machine.
+
+In case that certain widgets aren't rendered properly, make sure to enable the appropriate jupyter extensions
+
+```
+    $ jupyter nbextension enable --py widgetsnbextension
+```
+
+## Running
+
+Launch your local jupyter installation with
+
+```
+    $ jupyter notebook
+```
+
+## Examples
+
+### Load the required module
+
+Before you start, you will need to import the required reixs package, enable bokeh plotting, and set the base directory.
+
+```
+## Define base directory
+basedir = "/home/braun/ownCloud/Beamtime/example_data/"
+
+## Setup necessarry inputs
+from reixs.LoadData import *
+from bokeh.io import show, output_notebook
+output_notebook(hide_banner=True)
+```
+
+### 1d plots
+
+#### General Loader1d
+
+```
+sca = Load1d()
+sca.load(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4)  # Loads multiple scans individually
+sca.add(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4)  # Adds multiple scans
+sca.subtract(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4,norm=False) # Subtracts scans from the first scan
+sca.xlim(lower_lim,upper_lim) # Sets the horizontal axis plot region
+sca.ylim(lower_lim,upper_lim) # Sets the vertical axis plot region
+sca.plot_legend("pos string as per bokeh") # Determines a specific legend position
+sca.vline(position) # Draws a vertical line
+sca.hline(position) # Draws a horizontal line
+sca.label(pos_x,pos_y,'Text') # Adds a label to the plot
+sca.plot() # Plots the defined object
+sca.exporter() # Exports the data by calling an exporter widget
+```
+
+0. Create "Loader" object
+
+1. Specify the variable for the base directory (basedir)
+
+2. Enter the file name of the scan to analyse ('FileName.dat')
+
+3. Options for **x_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+- _MCP Energy_ (uncalibrated)
+- _SDD Energy_ (uncalibrated)
+- _XEOL Energy_ (uncalibrated, actually the wavelength scale)
+- _Points_ (by index)
+
+4. Options for **y_stream** quantities include:
+- All quantities in the header file
+- _TEY_ (Total Electron Yield: sample normalized by mesh)
+- _TFY_ (Total Fluorescence Yield, normalized by mesh)
+- _PFY_ and _iPFY_ (Partial Fluorescence Yield and Inverse Partial Fluorescence Yield, both normalized by mesh)
+  Specify ROI with brackets, either by XAS edge or energy:
+  e.g. _PFY[O]_ for PFY at the O K edge
+  e.g. _PFY[490:560]_ for PFY from 490eV to 560eV
+- _specPFY_ (spectrometer PFY, normalized by mesh)
+  specify energy range
+  e.g. specPFY[500:520]
+- _XES_ and _rXES_ (X-Ray emission and resonant x-ray emission at selected energies from the spectrometer MCP data)
+  e.g. rXES[560:565]
+- _XRF_ and _rXRF_ (X-Ray fluorescence and resonant x-ray fluorescence at selected energies from the SDD data)
+  e.g. rXRF[550:570]
+- _XEOL_ and _rXEOL_ (XEOL data from the optical spectrometer)
+- _POY_ and _TOY_ (Partial optical yield and total optical yield, normalized by mesh)
+  e.g. POY[300:750]
+- _EY_ or _Sample_ (Sample current, not normalized by mesh)
+- _Mesh_ (Mesh current)
+- _ET_ (Energy Transfer data, integrates over energy loss ROI and probes constant final states, sometimes referred to as CET scan)
+  specify energy transfer region
+  e.g. ET[-2:5] to probe mostly scattering close to the elastic line
+- _rLOSS_ (Resonantly excited emission data on energy loss scale, integrates over incident energy ROIS and probes constant intermediate states, sometimes referred to as CIE scan)
+  specify incident energy region
+  e.g. rLOSS[620:640]
+
+5. List all scans to analyse (comma-separated)
+
+6. Set optional flags. Options include:
+- _norm_ (Normalizes to [0,1])
+- _xcoffset_ (Defines a constant shift in the x-stream)
+- _xoffset_ (Takes a list of tuples and defines a polynomial fit of the x-stream)
+- _ycoffset_ (Defines a constant shift in the y-stream)
+- _yoffset_ (Takes a list of tuples and defines a polynomial fit of the y-stream)
+  e.g. offset = [(100,102),(110,112),(120,121)]
+- _background_ (Subtracts a XEOL background from XEOL scans)
+  Set to True, uses the getXEOLback function with the background data stored (only supported with HDF5)
+  Specify scan number, subtracts the XEOL scan taken at this particular scan
+- _energyloss_ (Transfers the resultant MCP scale to energy loss 
+  Set to True, then takes mean of mono energy array
+  Specify float with the incident photon energy
+- _grid_x_ (Takes a list with three arguments to apply 1d interpolation gridding)
+  e.g. grid_x = [Start Energy, Stop Energy, Delta]
+- _savgol_ (Takes a list with two or three arguments to apply data smoothing and derivatives)
+  e.g. savgol = [Window length, Polynomial order, deriavtive] as specified in the scipy Savitzky-Golay filter
+- _binsize_ (int, allows to perform data binning to improve Signal-to-Noise)
+- _legend_items_ (dict={scan_number:"name"}, overwrites generic legend names; works for the _load_ method)
+- _legend_item_ (str, overwrites generic legend name in the _add_/_subtract_ method)
+
+#### Absorption Scans
+
+```
+xas = XASLoader()
+xas.load(basedir,'Plate2a.dat','TEY',1,4,6)
+xas.load(basedir,'Plate2a.dat','PFY[O]',1,4)
+xas.add(basedir,'Plate2a.dat','PFY[500:520]',1,4)
+xas.subtract(basedir,'Plate2a.dat','specPFY[500:520]',1,4,6)
+xas.plot()
+xas.exporter()
+```
+
+#### Emission Scans (MCP)
+
+```
+xes = XESLoader()
+# Options: XES, rXES
+xes.load(basedir,'Plate2a.dat','XES',3,xoffset=[(515,520),(520,525),(530,535)])
+xes.load(basedir,'Plate2a.dat','rXES[520:560]',4)
+xes.add(basedir,'Plate2a.dat','XES',1,4)
+xes.subtract(basedir,'Plate2a.dat','XES',1,4)
+xes.plot()
+xes.exporter()
+```
+
+#### XRF Scans (SDD)
+
+```
+xrf = XRFLoader()
+# Options XRF,rXRF
+xrf.load(basedir,'Plate2a.dat','XRF',3)
+xrf.load(basedir,'Plate2a.dat','rXRF[520:560]',4)
+xrf.add(basedir,'Plate2a.dat','XRF',1,4,)
+xrf.subtract(basedir,'Plate2a.dat','XRF',1,4)
+xrf.plot()
+xrf.exporter()
+```
+
+#### XEOL Scans (Optical Spectrometer)
+
+```
+xeol = XEOLLoader()
+#Options: XEOL, rXEOL
+xeol.load(basedir,'RIXS_ES_QA.dat','XEOL',1,2,3,4,background=3)
+xeol.load(basedir,'RIXS_ES_QA.dat','XEOL',1,2,3,4,background=True)
+xeol.plot()
+```
+
+### 2d Images
+
+#### General loader for MCA detector data
+
+Note: Can only load one scan at a time!
+
+```
+load2d = Load2d()
+load2d.load(basedir,'Filename.dat','x_stream','y_stream','detector',1)
+load2d.plot()
+load2d.exporter()
+```
+
+0. Create "Loader" object
+
+1. Specify the variable for the base directory (basedir)
+
+2. Enter the file name of the scan to analyse ('FileName.dat')
+
+3. Options for **x_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+
+4. Options for **y_stream** quantities include:
+- _SDD Energy_ (Energy scale of the SDD detector)
+- _MCP Energy_ (Energy scale of the MCP detector)
+- _XEOL Energy_ (Wavelength scale of the XEOL optical spectrometer)
+
+5. Options for **detector** quantities include:
+- _SDD_ (SDD detector MCA)
+- _MCP_ (MCP detector MCA)
+- _XEOL_ (XEOL optical spectrometer MCA)
+
+6. List all scans to analyse (comma-separated)
+
+7. Set optional flags. Options include:
+- _norm_ (Normalizes to [0,1])
+- _xcoffset_ (Defines a constant shift in the x-stream)
+- _xoffset_ (Takes a list of tuples and defines a polynomial fit of the x-stream)
+- _ycoffset_ (Defines a constant shift in the y-stream)
+- _yoffset_ (Takes a list of tuples and defines a polynomial fit of the y-stream)
+  e.g. offset = [(100,102),(110,112),(120,121)]
+- _background_ (Subtracts a XEOL background from XEOL scans)
+  Set to True, uses the getXEOLback function with the background data stored (only supported with HDF5)
+  Specify scan number, subtracts the XEOL scan taken at this particular scan
+- _energyloss_ (Transfers the excitation-emission map to energy loss scale
+- _grid_x_ (Takes a list with three arguments to apply 1d interpolation gridding)
+  e.g. grid_x = [Start Energy, Stop Energy, Delta]
+
+#### EEMs (normalized by mesh current, special version of the general 2d image loader)
+
+Note: Can only load one scan at a time!
+
+```
+eems = EEMsLoader()
+eems.load(basedir,'Plate2a.dat','SDD',1)
+eems.load(basedir,'Plate2a.dat','MCP',1)
+eems.load(basedir,'RIXS_ES_QA.dat','XEOL',2,background=3)
+eems.plot()
+eems.exporter()
+```
+
+### Mesh Scans (Plots a 2d histogram)
+
+```
+mesh = LoadMesh()
+mesh.load(basedir,'Filename.txt','x_stream','y_stream','z_stream',24)
+mesh.plot()
+mesh.exporter()
+```
+
+0. Create "Loader" object
+
+1. Specify the variable for the base directory (basedir)
+
+2. Enter the file name of the scan to analyse ('FileName.dat')
+
+3. Options for **x_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+- _SDD Energy_ (Energy scale of the SDD detector)
+- _MCP Energy_ (Energy scale of the MCP detector)
+- _XEOL Energy_ (Wavelength scale of the XEOL optical spectrometer)
+
+4. Options for **y_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+- _SDD Energy_ (Energy scale of the SDD detector)
+- _MCP Energy_ (Energy scale of the MCP detector)
+- _XEOL Energy_ (Wavelength scale of the XEOL optical spectrometer)
+
+5. Options for **z_stream** quantities include:
+- All quantities in the header file
+- All special quantities as specified for the Load1d() function
+
+6. List all scans to analyse (comma-separated)
+
+7. Set optional flags. Options include:
+- _norm_ (Normalizes to [0,1])
+- _xcoffset_ (Defines a constant shift in the x-stream)
+- _xoffset_ (Takes a list of tuples and defines a polynomial fit of the x-stream)
+- _ycoffset_ (Defines a constant shift in the y-stream)
+- _yoffset_ (Takes a list of tuples and defines a polynomial fit of the y-stream)
+  e.g. offset = [(100,102),(110,112),(120,121)]
+- _background_ (Subtracts a XEOL background from XEOL scans)
+  Set to True, uses the getXEOLback function with the background data stored (only supported with HDF5)
+  Specify scan number, subtracts the XEOL scan taken at this particular scan
+
+
+%package help
+Summary:	Development documents and examples for reixs
+Provides:	python3-reixs-doc
+%description help
+# CLS REIXS Analysis
+
+This is a library to analyse, plot, and export REIXS beamline data. The package is meant to provide a framework to load data into jupyter and enable data interaction.
+
+Further [beamline information](https://reixs.lightsource.ca/) is available on the Website of the Canadian Light Source.
+
+## Installation
+
+Install the package from PyPi with the pip package manager. This is the recommended way to obtain a copy for your local machine and will install all required dependencies.
+
+```
+    $ pip install reixs
+```
+
+You will also need [Jupyter Notebook](https://github.com/jupyter) together with python 3 on your local machine.
+
+In case that certain widgets aren't rendered properly, make sure to enable the appropriate jupyter extensions
+
+```
+    $ jupyter nbextension enable --py widgetsnbextension
+```
+
+## Running
+
+Launch your local jupyter installation with
+
+```
+    $ jupyter notebook
+```
+
+## Examples
+
+### Load the required module
+
+Before you start, you will need to import the required reixs package, enable bokeh plotting, and set the base directory.
+
+```
+## Define base directory
+basedir = "/home/braun/ownCloud/Beamtime/example_data/"
+
+## Setup necessarry inputs
+from reixs.LoadData import *
+from bokeh.io import show, output_notebook
+output_notebook(hide_banner=True)
+```
+
+### 1d plots
+
+#### General Loader1d
+
+```
+sca = Load1d()
+sca.load(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4)  # Loads multiple scans individually
+sca.add(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4)  # Adds multiple scans
+sca.subtract(basedir,'FileName.dat','x_stream','y_stream',1,2,3,4,norm=False) # Subtracts scans from the first scan
+sca.xlim(lower_lim,upper_lim) # Sets the horizontal axis plot region
+sca.ylim(lower_lim,upper_lim) # Sets the vertical axis plot region
+sca.plot_legend("pos string as per bokeh") # Determines a specific legend position
+sca.vline(position) # Draws a vertical line
+sca.hline(position) # Draws a horizontal line
+sca.label(pos_x,pos_y,'Text') # Adds a label to the plot
+sca.plot() # Plots the defined object
+sca.exporter() # Exports the data by calling an exporter widget
+```
+
+0. Create "Loader" object
+
+1. Specify the variable for the base directory (basedir)
+
+2. Enter the file name of the scan to analyse ('FileName.dat')
+
+3. Options for **x_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+- _MCP Energy_ (uncalibrated)
+- _SDD Energy_ (uncalibrated)
+- _XEOL Energy_ (uncalibrated, actually the wavelength scale)
+- _Points_ (by index)
+
+4. Options for **y_stream** quantities include:
+- All quantities in the header file
+- _TEY_ (Total Electron Yield: sample normalized by mesh)
+- _TFY_ (Total Fluorescence Yield, normalized by mesh)
+- _PFY_ and _iPFY_ (Partial Fluorescence Yield and Inverse Partial Fluorescence Yield, both normalized by mesh)
+  Specify ROI with brackets, either by XAS edge or energy:
+  e.g. _PFY[O]_ for PFY at the O K edge
+  e.g. _PFY[490:560]_ for PFY from 490eV to 560eV
+- _specPFY_ (spectrometer PFY, normalized by mesh)
+  specify energy range
+  e.g. specPFY[500:520]
+- _XES_ and _rXES_ (X-Ray emission and resonant x-ray emission at selected energies from the spectrometer MCP data)
+  e.g. rXES[560:565]
+- _XRF_ and _rXRF_ (X-Ray fluorescence and resonant x-ray fluorescence at selected energies from the SDD data)
+  e.g. rXRF[550:570]
+- _XEOL_ and _rXEOL_ (XEOL data from the optical spectrometer)
+- _POY_ and _TOY_ (Partial optical yield and total optical yield, normalized by mesh)
+  e.g. POY[300:750]
+- _EY_ or _Sample_ (Sample current, not normalized by mesh)
+- _Mesh_ (Mesh current)
+- _ET_ (Energy Transfer data, integrates over energy loss ROI and probes constant final states, sometimes referred to as CET scan)
+  specify energy transfer region
+  e.g. ET[-2:5] to probe mostly scattering close to the elastic line
+- _rLOSS_ (Resonantly excited emission data on energy loss scale, integrates over incident energy ROIS and probes constant intermediate states, sometimes referred to as CIE scan)
+  specify incident energy region
+  e.g. rLOSS[620:640]
+
+5. List all scans to analyse (comma-separated)
+
+6. Set optional flags. Options include:
+- _norm_ (Normalizes to [0,1])
+- _xcoffset_ (Defines a constant shift in the x-stream)
+- _xoffset_ (Takes a list of tuples and defines a polynomial fit of the x-stream)
+- _ycoffset_ (Defines a constant shift in the y-stream)
+- _yoffset_ (Takes a list of tuples and defines a polynomial fit of the y-stream)
+  e.g. offset = [(100,102),(110,112),(120,121)]
+- _background_ (Subtracts a XEOL background from XEOL scans)
+  Set to True, uses the getXEOLback function with the background data stored (only supported with HDF5)
+  Specify scan number, subtracts the XEOL scan taken at this particular scan
+- _energyloss_ (Transfers the resultant MCP scale to energy loss 
+  Set to True, then takes mean of mono energy array
+  Specify float with the incident photon energy
+- _grid_x_ (Takes a list with three arguments to apply 1d interpolation gridding)
+  e.g. grid_x = [Start Energy, Stop Energy, Delta]
+- _savgol_ (Takes a list with two or three arguments to apply data smoothing and derivatives)
+  e.g. savgol = [Window length, Polynomial order, deriavtive] as specified in the scipy Savitzky-Golay filter
+- _binsize_ (int, allows to perform data binning to improve Signal-to-Noise)
+- _legend_items_ (dict={scan_number:"name"}, overwrites generic legend names; works for the _load_ method)
+- _legend_item_ (str, overwrites generic legend name in the _add_/_subtract_ method)
+
+#### Absorption Scans
+
+```
+xas = XASLoader()
+xas.load(basedir,'Plate2a.dat','TEY',1,4,6)
+xas.load(basedir,'Plate2a.dat','PFY[O]',1,4)
+xas.add(basedir,'Plate2a.dat','PFY[500:520]',1,4)
+xas.subtract(basedir,'Plate2a.dat','specPFY[500:520]',1,4,6)
+xas.plot()
+xas.exporter()
+```
+
+#### Emission Scans (MCP)
+
+```
+xes = XESLoader()
+# Options: XES, rXES
+xes.load(basedir,'Plate2a.dat','XES',3,xoffset=[(515,520),(520,525),(530,535)])
+xes.load(basedir,'Plate2a.dat','rXES[520:560]',4)
+xes.add(basedir,'Plate2a.dat','XES',1,4)
+xes.subtract(basedir,'Plate2a.dat','XES',1,4)
+xes.plot()
+xes.exporter()
+```
+
+#### XRF Scans (SDD)
+
+```
+xrf = XRFLoader()
+# Options XRF,rXRF
+xrf.load(basedir,'Plate2a.dat','XRF',3)
+xrf.load(basedir,'Plate2a.dat','rXRF[520:560]',4)
+xrf.add(basedir,'Plate2a.dat','XRF',1,4,)
+xrf.subtract(basedir,'Plate2a.dat','XRF',1,4)
+xrf.plot()
+xrf.exporter()
+```
+
+#### XEOL Scans (Optical Spectrometer)
+
+```
+xeol = XEOLLoader()
+#Options: XEOL, rXEOL
+xeol.load(basedir,'RIXS_ES_QA.dat','XEOL',1,2,3,4,background=3)
+xeol.load(basedir,'RIXS_ES_QA.dat','XEOL',1,2,3,4,background=True)
+xeol.plot()
+```
+
+### 2d Images
+
+#### General loader for MCA detector data
+
+Note: Can only load one scan at a time!
+
+```
+load2d = Load2d()
+load2d.load(basedir,'Filename.dat','x_stream','y_stream','detector',1)
+load2d.plot()
+load2d.exporter()
+```
+
+0. Create "Loader" object
+
+1. Specify the variable for the base directory (basedir)
+
+2. Enter the file name of the scan to analyse ('FileName.dat')
+
+3. Options for **x_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+
+4. Options for **y_stream** quantities include:
+- _SDD Energy_ (Energy scale of the SDD detector)
+- _MCP Energy_ (Energy scale of the MCP detector)
+- _XEOL Energy_ (Wavelength scale of the XEOL optical spectrometer)
+
+5. Options for **detector** quantities include:
+- _SDD_ (SDD detector MCA)
+- _MCP_ (MCP detector MCA)
+- _XEOL_ (XEOL optical spectrometer MCA)
+
+6. List all scans to analyse (comma-separated)
+
+7. Set optional flags. Options include:
+- _norm_ (Normalizes to [0,1])
+- _xcoffset_ (Defines a constant shift in the x-stream)
+- _xoffset_ (Takes a list of tuples and defines a polynomial fit of the x-stream)
+- _ycoffset_ (Defines a constant shift in the y-stream)
+- _yoffset_ (Takes a list of tuples and defines a polynomial fit of the y-stream)
+  e.g. offset = [(100,102),(110,112),(120,121)]
+- _background_ (Subtracts a XEOL background from XEOL scans)
+  Set to True, uses the getXEOLback function with the background data stored (only supported with HDF5)
+  Specify scan number, subtracts the XEOL scan taken at this particular scan
+- _energyloss_ (Transfers the excitation-emission map to energy loss scale
+- _grid_x_ (Takes a list with three arguments to apply 1d interpolation gridding)
+  e.g. grid_x = [Start Energy, Stop Energy, Delta]
+
+#### EEMs (normalized by mesh current, special version of the general 2d image loader)
+
+Note: Can only load one scan at a time!
+
+```
+eems = EEMsLoader()
+eems.load(basedir,'Plate2a.dat','SDD',1)
+eems.load(basedir,'Plate2a.dat','MCP',1)
+eems.load(basedir,'RIXS_ES_QA.dat','XEOL',2,background=3)
+eems.plot()
+eems.exporter()
+```
+
+### Mesh Scans (Plots a 2d histogram)
+
+```
+mesh = LoadMesh()
+mesh.load(basedir,'Filename.txt','x_stream','y_stream','z_stream',24)
+mesh.plot()
+mesh.exporter()
+```
+
+0. Create "Loader" object
+
+1. Specify the variable for the base directory (basedir)
+
+2. Enter the file name of the scan to analyse ('FileName.dat')
+
+3. Options for **x_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+- _SDD Energy_ (Energy scale of the SDD detector)
+- _MCP Energy_ (Energy scale of the MCP detector)
+- _XEOL Energy_ (Wavelength scale of the XEOL optical spectrometer)
+
+4. Options for **y_stream** quantities include:
+- All quantities in the header file
+- _Mono Energy_ for the excitation energy
+- _SDD Energy_ (Energy scale of the SDD detector)
+- _MCP Energy_ (Energy scale of the MCP detector)
+- _XEOL Energy_ (Wavelength scale of the XEOL optical spectrometer)
+
+5. Options for **z_stream** quantities include:
+- All quantities in the header file
+- All special quantities as specified for the Load1d() function
+
+6. List all scans to analyse (comma-separated)
+
+7. Set optional flags. Options include:
+- _norm_ (Normalizes to [0,1])
+- _xcoffset_ (Defines a constant shift in the x-stream)
+- _xoffset_ (Takes a list of tuples and defines a polynomial fit of the x-stream)
+- _ycoffset_ (Defines a constant shift in the y-stream)
+- _yoffset_ (Takes a list of tuples and defines a polynomial fit of the y-stream)
+  e.g. offset = [(100,102),(110,112),(120,121)]
+- _background_ (Subtracts a XEOL background from XEOL scans)
+  Set to True, uses the getXEOLback function with the background data stored (only supported with HDF5)
+  Specify scan number, subtracts the XEOL scan taken at this particular scan
+
+
+%prep
+%autosetup -n reixs-0.5.11
+
+%build
+%py3_build
+
+%install
+%py3_install
+install -d -m755 %{buildroot}/%{_pkgdocdir}
+if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
+if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
+if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
+if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
+pushd %{buildroot}
+if [ -d usr/lib ]; then
+	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/lib64 ]; then
+	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/bin ]; then
+	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/sbin ]; then
+	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+touch doclist.lst
+if [ -d usr/share/man ]; then
+	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
+fi
+popd
+mv %{buildroot}/filelist.lst .
+mv %{buildroot}/doclist.lst .
+
+%files -n python3-reixs -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Thu May 18 2023 Python_Bot <Python_Bot@openeuler.org> - 0.5.11-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..319c244
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+54daa93cf09ad2ef08bef01b02a655c3  reixs-0.5.11.tar.gz