SusMat-SWAXS 2.1.3__tar.gz

susmat_swaxs-2.1.3/PKG-INFO

@@ -0,0 +1,173 @@
+Metadata-Version: 2.3
+Name: SusMat-SWAXS
+Version: 2.1.3
+Summary: A collection of python scripts for uploading analytical data to iRODS
+Author: Samuel Eyley
+Author-email: Samuel Eyley <susmat-swaxspypi.xepsj@simplelogin.com>
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Dist: pyfai>2024.10.0
+Requires-Dist: pyopencl
+Requires-Dist: click
+Requires-Dist: pyside6
+Requires-Dist: h5py
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: sympy
+Requires-Dist: fabio
+Requires-Dist: hdf5plugin
+Requires-Dist: pillow
+Requires-Dist: fairmat-readers-xrd>=0.0.8
+Requires-Python: >=3.12
+Project-URL: Homepage, https://github.com/Sustainable-Materials-Lab/SusMat-SWAXS
+Project-URL: Issues, https://github.com/Sustainable-Materials-Lab/SusMat-SWAXS/issues
+Description-Content-Type: text/markdown
+
+# SWAXS tools
+
+## Description
+This is a collection of scripts to perform data conversion and integration on X-ray scattering data, specifically for data collected on the Xenocs Xeuss SWAXS instrument.
+
+**Available tools:**
+- `sm-datconv` - Converts Xenocs format 1D data (.dat) to TOPAS compatible .xye format
+- `sm-edfh5` - Convert EDF files to HDF5 format with metadata preservation
+- `sm-saxsint` - Integrate 2D SAXS data from Xenocs Xeuss instruments with background subtraction
+- `sm-waxsint` - Integrate 2D WAXS data from Xenocs Xeuss instruments with absorption correction
+- `sm-spharm` - Visualize spherical harmonics functions from TOPAS coefficients
+
+## Installation
+Install in a virtual environment to avoid dependency conflicts:
+
+```bash
+pip install SusMat-SWAXS
+```
+
+
+## Usage
+All scripts are available as command-line tools after installation. Use the `--help` flag with any command to see detailed usage information.
+
+### sm-datconv
+Converts Xenocs format 1D data (.dat) to TOPAS compatible .xye format.
+
+**Input:** `.dat` file with tab-separated columns for q, I(q) (and optionally sigma).
+
+**Usage:**
+```bash
+sm-datconv <filename_without_extension>
+```
+
+**Output:** `.xye` file with tab-separated columns for 2θ, I, and error (if present in input).
+
+**Batch processing example (PowerShell):**
+```powershell
+Get-ChildItem -Filter *.dat | ForEach-Object -Process {sm-datconv $_.BaseName}
+```
+
+### sm-xrdmlconv
+Converts Malvern PANalytical format 1D data (.xrdml) to TOPAS compatible .xy format.
+
+**Input:** `.xrdml` file .
+
+**Usage:**
+```bash
+sm-xrdmlconv <filename_without_extension>
+```
+
+**Output:** `.xy` file with tab-separated columns for 2θ and I and a `.json` file containing metadata.
+
+### sm-edfh5
+Convert multiple EDF files to a single HDF5 file with metadata preservation.
+
+**Usage:**
+```bash
+sm-edfh5 <path to directory containing edf files>
+```
+
+### sm-saxsint
+Integrate 2D SAXS data from Xenocs Xeuss instruments with background subtraction and absorption correction.
+
+**Usage:**
+```bash
+sm-saxsint <sample.edf> <mask.edf> [OPTIONS]
+```
+
+**Key options:**
+- `--poni <file.poni>` - PONI calibration file
+- `--background <bkg.edf>` - Background file for subtraction
+- `--bkg_factor <float>` - Background scaling factor (default: 1.0)
+- `--unit <q|2th>` - Radial unit for integration (default: q)
+- `--xmin <float>` - Minimum q value (default: 0.004)
+- `--xmax <float>` - Maximum q value (default: 0.7)
+- `--opencl` - Use OpenCL acceleration (requires pyopencl)
+- `--raw2D` - Display 2D image in lab frame
+
+**Output:** 
+- `*_1D.dat` - Integrated 1D data
+- `*_subtracted.dat` - Background-subtracted data
+- `*.svg` - Visualization plot
+
+### sm-waxsint
+Integrate 2D WAXS data from Xenocs Xeuss instruments with absorption correction.
+
+**Usage:**
+```bash
+sm-waxsint <sample.edf> <mask.edf> [OPTIONS]
+```
+
+**Key options:**
+- `--poni <file.poni>` - PONI calibration file
+- `--background <bkg.edf>` - Background file for subtraction
+- `--bkg_factor <float>` - Background scaling factor (default: 1.0)
+- `--unit <q|2th>` - Radial unit for integration (default: q)
+- `--xmin <float>` - Minimum q value (default: 0.36)
+- `--xmax <float>` - Maximum q value (default: 3.8)
+- `--lac <float>` - Linear absorption coefficient in cm⁻¹ for thickness correction
+- `--thickness <float>` - Sample thickness in cm for transmission correction
+- `--noabs` - Disable absorption correction
+- `--opencl` - Use OpenCL acceleration (requires pyopencl)
+- `--raw2D` - Display 2D image in lab frame
+
+**Output:**
+- `*_1D.dat` - Integrated 1D data
+- `*_subtracted.dat` - Background-subtracted, absorption-corrected data
+- `*.svg` - Visualization plot
+
+### sm-spharm
+Visualize spherical harmonics functions using coefficients from TOPAS academic output files.
+
+**Usage:**
+```bash
+sm-spharm C00 C20 C22P C22M C40 C42P C42M C44P C44M C60 C62P C62M C64P C64M C66P C66M C80 C82P C82M C84P C84M C86P C86M C88P C88M [OPTIONS]
+```
+
+**Arguments:** 25 spherical harmonics coefficients (c00 through c88m) from TOPAS output file
+
+**Options:**
+- `--output <filename>` / `-o <filename>` - Output filename for the plot (default: sph_harm.svg)
+- `--resolution <int>` / `-r <int>` - Angular resolution for the plot (default: 200)
+
+**Example:**
+```bash
+sm-spharm 1 -0.54889 0.48504 0.74711 0.79916 -0.33178 0.16323 0.45369 \
+          -0.29782 -0.29214 -0.43949 0.01524 0.09042 0.85340 0.40316 \
+          -0.01881 1.47673 -0.55751 -0.68970 0.02621 -0.06565 -0.56472 \
+          1.00981 -0.12339 -0.25831 --output my_spherical_harmonics.svg
+```
+
+**Output:** 3D visualization plot showing the spherical harmonics function in real space
+
+## Support
+Submit an issue on github: https://github.com/Sustainable-Materials-Lab/SusMat-SWAXS
+
+## Contributing
+Contact Samuel Eyley if you are interested in contributing.
+
+## Authors and acknowledgment
+Originally authored by Samuel Eyley. 
+
+Significant portions of code were developed with the help of Github Copilot (2025).
+
+## License
+MIT License

susmat_swaxs-2.1.3/README.md

@@ -0,0 +1,146 @@
+# SWAXS tools
+
+## Description
+This is a collection of scripts to perform data conversion and integration on X-ray scattering data, specifically for data collected on the Xenocs Xeuss SWAXS instrument.
+
+**Available tools:**
+- `sm-datconv` - Converts Xenocs format 1D data (.dat) to TOPAS compatible .xye format
+- `sm-edfh5` - Convert EDF files to HDF5 format with metadata preservation
+- `sm-saxsint` - Integrate 2D SAXS data from Xenocs Xeuss instruments with background subtraction
+- `sm-waxsint` - Integrate 2D WAXS data from Xenocs Xeuss instruments with absorption correction
+- `sm-spharm` - Visualize spherical harmonics functions from TOPAS coefficients
+
+## Installation
+Install in a virtual environment to avoid dependency conflicts:
+
+```bash
+pip install SusMat-SWAXS
+```
+
+
+## Usage
+All scripts are available as command-line tools after installation. Use the `--help` flag with any command to see detailed usage information.
+
+### sm-datconv
+Converts Xenocs format 1D data (.dat) to TOPAS compatible .xye format.
+
+**Input:** `.dat` file with tab-separated columns for q, I(q) (and optionally sigma).
+
+**Usage:**
+```bash
+sm-datconv <filename_without_extension>
+```
+
+**Output:** `.xye` file with tab-separated columns for 2θ, I, and error (if present in input).
+
+**Batch processing example (PowerShell):**
+```powershell
+Get-ChildItem -Filter *.dat | ForEach-Object -Process {sm-datconv $_.BaseName}
+```
+
+### sm-xrdmlconv
+Converts Malvern PANalytical format 1D data (.xrdml) to TOPAS compatible .xy format.
+
+**Input:** `.xrdml` file .
+
+**Usage:**
+```bash
+sm-xrdmlconv <filename_without_extension>
+```
+
+**Output:** `.xy` file with tab-separated columns for 2θ and I and a `.json` file containing metadata.
+
+### sm-edfh5
+Convert multiple EDF files to a single HDF5 file with metadata preservation.
+
+**Usage:**
+```bash
+sm-edfh5 <path to directory containing edf files>
+```
+
+### sm-saxsint
+Integrate 2D SAXS data from Xenocs Xeuss instruments with background subtraction and absorption correction.
+
+**Usage:**
+```bash
+sm-saxsint <sample.edf> <mask.edf> [OPTIONS]
+```
+
+**Key options:**
+- `--poni <file.poni>` - PONI calibration file
+- `--background <bkg.edf>` - Background file for subtraction
+- `--bkg_factor <float>` - Background scaling factor (default: 1.0)
+- `--unit <q|2th>` - Radial unit for integration (default: q)
+- `--xmin <float>` - Minimum q value (default: 0.004)
+- `--xmax <float>` - Maximum q value (default: 0.7)
+- `--opencl` - Use OpenCL acceleration (requires pyopencl)
+- `--raw2D` - Display 2D image in lab frame
+
+**Output:** 
+- `*_1D.dat` - Integrated 1D data
+- `*_subtracted.dat` - Background-subtracted data
+- `*.svg` - Visualization plot
+
+### sm-waxsint
+Integrate 2D WAXS data from Xenocs Xeuss instruments with absorption correction.
+
+**Usage:**
+```bash
+sm-waxsint <sample.edf> <mask.edf> [OPTIONS]
+```
+
+**Key options:**
+- `--poni <file.poni>` - PONI calibration file
+- `--background <bkg.edf>` - Background file for subtraction
+- `--bkg_factor <float>` - Background scaling factor (default: 1.0)
+- `--unit <q|2th>` - Radial unit for integration (default: q)
+- `--xmin <float>` - Minimum q value (default: 0.36)
+- `--xmax <float>` - Maximum q value (default: 3.8)
+- `--lac <float>` - Linear absorption coefficient in cm⁻¹ for thickness correction
+- `--thickness <float>` - Sample thickness in cm for transmission correction
+- `--noabs` - Disable absorption correction
+- `--opencl` - Use OpenCL acceleration (requires pyopencl)
+- `--raw2D` - Display 2D image in lab frame
+
+**Output:**
+- `*_1D.dat` - Integrated 1D data
+- `*_subtracted.dat` - Background-subtracted, absorption-corrected data
+- `*.svg` - Visualization plot
+
+### sm-spharm
+Visualize spherical harmonics functions using coefficients from TOPAS academic output files.
+
+**Usage:**
+```bash
+sm-spharm C00 C20 C22P C22M C40 C42P C42M C44P C44M C60 C62P C62M C64P C64M C66P C66M C80 C82P C82M C84P C84M C86P C86M C88P C88M [OPTIONS]
+```
+
+**Arguments:** 25 spherical harmonics coefficients (c00 through c88m) from TOPAS output file
+
+**Options:**
+- `--output <filename>` / `-o <filename>` - Output filename for the plot (default: sph_harm.svg)
+- `--resolution <int>` / `-r <int>` - Angular resolution for the plot (default: 200)
+
+**Example:**
+```bash
+sm-spharm 1 -0.54889 0.48504 0.74711 0.79916 -0.33178 0.16323 0.45369 \
+          -0.29782 -0.29214 -0.43949 0.01524 0.09042 0.85340 0.40316 \
+          -0.01881 1.47673 -0.55751 -0.68970 0.02621 -0.06565 -0.56472 \
+          1.00981 -0.12339 -0.25831 --output my_spherical_harmonics.svg
+```
+
+**Output:** 3D visualization plot showing the spherical harmonics function in real space
+
+## Support
+Submit an issue on github: https://github.com/Sustainable-Materials-Lab/SusMat-SWAXS
+
+## Contributing
+Contact Samuel Eyley if you are interested in contributing.
+
+## Authors and acknowledgment
+Originally authored by Samuel Eyley. 
+
+Significant portions of code were developed with the help of Github Copilot (2025).
+
+## License
+MIT License

susmat_swaxs-2.1.3/pyproject.toml

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+[build-system]
+requires = ["uv_build>=0.9.6,<0.10.0"]
+build-backend = "uv_build"
+
+[project]
+name = "SusMat-SWAXS"
+version = "2.1.3"
+authors = [
+  { name="Samuel Eyley", email="susmat-swaxspypi.xepsj@simplelogin.com" },
+]
+description = "A collection of python scripts for uploading analytical data to iRODS"
+readme = "README.md"
+requires-python = ">=3.12"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "pyfai>2024.10.0",
+    "pyopencl",
+    "click",
+    "pyside6",
+    "h5py",
+    "matplotlib",
+    "numpy",
+    "scipy",
+    "sympy",
+    "fabio",
+    "hdf5plugin",
+    "pillow",
+    "fairmat-readers-xrd>=0.0.8",
+]
+
+[project.urls]
+Homepage = "https://github.com/Sustainable-Materials-Lab/SusMat-SWAXS"
+Issues = "https://github.com/Sustainable-Materials-Lab/SusMat-SWAXS/issues"
+
+[project.scripts]
+sm-datconv = "smswaxs.dat_conv:cli"
+sm-xrdmlconv = "smswaxs.xrdml_conv:cli"
+sm-topasinit = "smswaxs.topas_init:cli"
+sm-edfh5 = "smswaxs.xeuss_edf_h5_multi:add_edfs_to_hdf5"
+sm-saxsint = "smswaxs.saxs_integration_xeuss:cli"
+sm-waxsint = "smswaxs.waxs_integration_xeuss:cli"
+sm-spharm = "smswaxs.sph_harm:cli"
+
+
+[tool.uv.build-backend]
+module-name = "smswaxs"

susmat_swaxs-2.1.3/src/smswaxs/__init__.py

@@ -0,0 +1,32 @@
+"""
+SusMat-SWAXS: A collection of python scripts for SWAXS data processing and conversion.
+
+This package provides tools for:
+- SAXS/WAXS data integration from Xenocs Xeuss instruments
+- Data format conversions (EDF to HDF5, TIFF, etc.)
+- Background subtraction and absorption corrections
+- Data visualization and analysis
+"""
+
+__version__ = "2.1.3"
+__author__ = "Samuel Eyley"
+__email__ = "samuel.eyley@kuleuven.be"
+
+# Import CLI functions for programmatic access
+from .dat_conv import cli as dat_conv_cli
+from .xeuss_edf_h5_multi import add_edfs_to_hdf5
+from .saxs_integration_xeuss import cli as saxs_integration_cli
+from .waxs_integration_xeuss import cli as waxs_integration_cli
+from .sph_harm import cli as sph_harm_cli
+
+# Make CLI functions available at package level
+__all__ = [
+    "__version__",
+    "__author__", 
+    "__email__",
+    "dat_conv_cli",
+    "add_edfs_to_hdf5", 
+    "saxs_integration_cli",
+    "waxs_integration_cli",
+    "sph_harm_cli"
+]

susmat_swaxs-2.1.3/src/smswaxs/dat_conv.py

@@ -0,0 +1,136 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu May  7 11:44:10 2015
+
+@author: u0092172
+"""
+import argparse as ap
+import re
+import numpy as np
+
+def get_line_number(phrase, file_name):
+    """Get the line number containing phrase"""
+    with open(file_name, encoding="utf-8") as f:
+        for i, line in enumerate(f, 1):
+            p = re.compile(phrase)
+            if p.match(line) is not None:
+                return i
+
+def get_number_lines(file_name):
+    """Get the number of lines in a file"""
+    with open(file_name, encoding="utf-8") as f:
+        lines = len(f.readlines())
+        return lines
+
+
+def cli():
+    """Convert dat files to xye format for use in TOPAS"""
+    parser = ap.ArgumentParser(description='Convert dat files to xye format for use in TOPAS')
+    parser.add_argument("input", help="Filename of the .dat (excl. ext.)")
+    parser.add_argument(
+        "--wavelength", help="Wavelength in Angstroms", default=float(1.54189))
+    parser.add_argument(
+        "--highscore", help="Output for highscore plus", action="store_true")
+    parser.add_argument(
+        "--exposure", help="Counting time (convert to counts from CPS)", type=float, default=1)
+    # parser.add_argument("--dat", help="convert from dat file", action="store_true")
+    parser.add_argument(
+        "--SAXS", help="output SAXS data (q and don't cut low angle)", action="store_true")
+    parser.add_argument(
+        "--renormalize", help="boost counts", action="store_true")
+    parser.add_argument("--clip", help="clip range", action="store_true")
+    parser.add_argument(
+        "--fullprof", help="general fullprof input", action="store_true")
+    parser.add_argument(
+        "--kratky", help="Generate Kratky plot columns", action="store_true")
+    parser.add_argument("--pyfai", help="pyfai input", action="store_true")
+    parser.add_argument(
+        "--zero", help="set minimum to zero", action="store_true")
+    args = parser.parse_args()  # map arguments to args
+
+    fname = args.input
+    if args.highscore is True:
+        ext = ".asc"
+    elif args.fullprof is True:
+        ext = "_FP.dat"
+    elif args.kratky is True:
+        ext = "_kratky.dat"
+    else:
+        ext = ".xye"
+
+    # Import the data
+
+    if args.kratky is True:
+        args.SAXS = True
+
+    if args.pyfai is True:
+        data = np.genfromtxt(fname, comments='#',
+                             usecols=(0, 1, 2), encoding="utf-8")
+    else:
+        head = get_line_number('.*q\\([AÅ].*', fname)
+        data = np.genfromtxt(fname, skip_header=head,
+                             usecols=(0, 1, 2), encoding="utf-8")
+
+    data = data[~np.isnan(data).any(axis=1)]
+
+    q = data[:, 0]
+    i = data[:, 1]
+    e = data[:, 2]
+
+    if args.pyfai is True:
+        ttheta = q
+        if args.clip is True:
+            start = np.where(ttheta > 5)[0][0]
+            ttheta = ttheta[start:]
+            i = i[start:]
+            e = e[start:]
+    elif args.SAXS is False:
+        # Calc 2theta
+
+        ttheta = 2*np.degrees(np.arcsin((q*args.wavelength)/(4*np.pi)))
+
+        # Clip the data to start at 5 degrees to remove excessive intensity
+        if args.clip is True:
+            start = np.where(ttheta > 5)[0][0]
+            ttheta = ttheta[start:]
+            i = i[start:]
+            e = e[start:]
+
+        # Convert i to counts
+    if args.renormalize is True:
+        i = i*args.exposure*1e11
+    else:
+        i = i*args.exposure
+
+    if min(i) < 0:
+        i -= min(i)
+
+    if args.zero is True:
+        i -= min(i)
+
+    if args.highscore is True:
+        out = np.column_stack((ttheta.flatten(), i.flatten()))
+    else:
+        if args.SAXS is False:
+            out = np.column_stack((ttheta.flatten(), i.flatten(), e.flatten()))
+        elif args.kratky is False:
+            out = np.column_stack((q.flatten(), i.flatten(), e.flatten()))
+        else:
+            q2i = (q**2)*i
+            q2sig = (q**2)*e
+            out = np.column_stack(
+                (q.flatten(), i.flatten(), q2i.flatten(), e.flatten(), q2sig.flatten()))
+
+    if args.fullprof is True:
+        head2 = 'XYDATA' + '\n' + 'INTER 0 0 2' + 4*'\n'
+    elif args.kratky is True:
+        head2 = "q I(q) q2I(q) sig(q) q2sig(q)"
+    else:
+        head2 = ''
+
+    np.savetxt(fname[:-4]+ext, out, delimiter=' ', fmt='%.10f',
+               header=head2, comments='', newline='\n')
+
+
+if __name__ == '__main__':
+    cli()

susmat_swaxs-2.1.3/src/smswaxs/saxs_integration.py

@@ -0,0 +1,142 @@
+# -*- coding: utf-8 -*-
+"""
+Spyder Editor
+
+This is a temporary script file.
+"""
+
+import h5py
+import hdf5plugin
+import pyFAI
+import fabio
+import numpy as np
+import os
+import glob
+import matplotlib.pyplot as plt
+from matplotlib.colors import LogNorm
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+import matplotlib.ticker as ticker
+import argparse as ap
+
+parser = ap.ArgumentParser(description=
+                           "Perform data reduction on hdf5 data from DESY")
+
+parser.add_argument("sample", help="sample file (.nxs)")
+
+parser.add_argument("mask", help="mask file (.edf)")
+parser.add_argument("poni", help="PONI configuration file (.poni)")
+parser.add_argument("--empty", help="empty file (.nxs)")
+parser.add_argument("--background", help="background file (.nxs)")
+
+parser.add_argument("--bkg_factor", help="background correction factor",type=float,default=float(1))
+parser.add_argument("--noscaling", help="background file (.nxs)",action="store_true")
+parser.add_argument("--autobkg", help="Automatic background scaling",action="store_true")
+args = parser.parse_args()
+
+#path = "/home/u0092172/Documents/"
+#folder = "DESY/"
+#sample = "GA5/GA5_2.nxs"
+#background = "water/water_2.nxs"
+mask = fabio.open(args.mask)
+poni = pyFAI.load(args.poni)#"config_saxs_sdetx_1500_12keV.poni")
+file = h5py.File(args.sample,'r')
+
+if args.noscaling == True:
+    transmission_sample = 1
+else:
+    transmission_sample = file['scan']['data']['beamstop_2'][()]/file['scan']['data']['ic1'][()]
+print("Sample transmission:"+str(round(transmission_sample,4)))
+
+temperature = str(round(file['scan']['data']['p62']['t95tempproglinkam']['eh.01']['temperature'][()],2))
+print("Sample temperature:"+temperature)
+
+
+data_1D = poni.integrate1d(file['scan']['data']['saxs_raw'][()][0]/transmission_sample,
+                           1000, filename=args.sample+"_"+temperature+'_1D.dat', correctSolidAngle=True,
+                                  method='csr_ocl', radial_range=(None), azimuth_range=(None),
+                                  unit="q_A^-1", mask=mask.data, normalization_factor=1.0,
+                                  metadata=None,error_model="poisson") 
+
+if args.background != None:
+    bkg = h5py.File(args.background,'r')
+    if args.noscaling == True:
+        transmission_bkg = 1
+    else:
+        transmission_bkg = bkg['scan']['data']['beamstop_2'][()]/bkg['scan']['data']['ic1'][()]
+    try:
+        temperature_bkg = str(round(bkg['scan']['data']['p62']['t95tempproglinkam']['eh.01']['temperature'][()],2))
+    except KeyError:
+        temperature_bkg = str(-1000)
+    print("Background transmission:"+str(round(transmission_bkg,4)))
+    print("Background temperature:"+temperature_bkg)
+    
+    bkg_1D = poni.integrate1d(bkg['scan']['data']['saxs_raw'][()][0]/transmission_bkg,
+                              1000, filename=args.sample+"_"+temperature+'_bkg1D.dat', correctSolidAngle=True,
+                                  method='csr_ocl', radial_range=(None), azimuth_range=(None),
+                                  unit="q_A^-1", mask=mask.data, normalization_factor=1.0,
+                                  metadata=None,error_model="poisson")
+    if args.autobkg == True:
+        print("Use automated background scaling with caution!")
+        if max(bkg_1D[1][:np.where(bkg_1D[0]>0.02)[0][0]]) > max(data_1D[1][:np.where(data_1D[0]>0.02)[0][0]]):
+            bkg_1D = [bkg_1D[0],bkg_1D[1],bkg_1D[2]]
+            bkg_1D[1] -=  max(bkg_1D[1][:np.where(bkg_1D[0]>0.02)[0][0]]) - max(data_1D[1][:np.where(data_1D[0]>0.02)[0][0]])
+else:
+    data_I = data_1D[1]
+    data_sig = abs(data_1D[2])
+if args.empty != None:
+    empty = h5py.File(args.empty,'r')
+    if args.noscaling == True:
+        transmission_empty = 1
+    else:
+        transmission_empty = empty['scan']['data']['beamstop_2'][()]/empty['scan']['data']['ic1'][()]
+    empty_1D = poni.integrate1d(empty['scan']['data']['saxs_raw'][()][0]/transmission_empty,
+                              1000, filename=args.sample+"_"+temperature+'_empty1D.dat', correctSolidAngle=True,
+                                  method='csr_ocl', radial_range=(None), azimuth_range=(None),
+                                  unit="q_A^-1", mask=mask.data, normalization_factor=1.0,
+                                  metadata=None,error_model="poisson")
+    if args.autobkg == True:
+        if max(empty_1D[1][:np.where(empty_1D[0]>0.02)[0][0]]) > max(data_1D[1][:np.where(data_1D[0]>0.02)[0][0]]):
+            empty_1D[1] -= max(empty_1D[1][:np.where(empty_1D[0]>0.02)[0][0]]) - max(data_1D[1][:np.where(data_1D[0]>0.02)[0][0]])
+    if args.background != None:
+        data_I = (data_1D[1]-empty_1D[1])-(bkg_1D[1]-empty_1D[1])
+        data_sig = abs(data_1D[2])+abs(empty_1D[2])+abs(bkg_1D[2])+abs(empty_1D[2])
+    else:
+        data_I = data_1D[1]-empty_1D[1]
+        data_sig = abs(data_1D[2])+abs(empty_1D[2])
+else:
+    if args.background == None:
+        data_I = data_1D[1]
+        data_sig = abs(data_1D[2])
+    else:
+        data_I = data_1D[1]-bkg_1D[1]
+        data_sig = abs(data_1D[2])+abs(bkg_1D[2])
+fig, ax = plt.subplots(figsize=(25,10),constrained_layout=True)
+"""fig1 = ax[0].imshow(data_cor,norm=LogNorm(vmin=1e-1, vmax=10**3),cmap=plt.get_cmap('plasma'))
+# fig1 = ax[0].imshow(data_cor,norm=LogNorm(vmin=300, vmax=10**5),cmap=plt.get_cmap('plasma'))
+# create an axes on the right side of ax. The width of cax will be 5%
+# of ax and the padding between cax and ax will be fixed at 0.05 inch.
+divider = make_axes_locatable(ax[0])
+cax = divider.append_axes("right", size="5%", pad=0.05)
+
+cbar = plt.colorbar(fig1, cax=cax)
+cbar.ax.tick_params(labelsize=25)
+
+ax[0].set_xlabel('pixel',fontsize=25)
+ax[0].set_ylabel('pixel',fontsize=25)
+ax[0].tick_params(labelsize=25)
+"""
+# fig2 = ax.plot(q, Intensity)
+#fig2 = ax.plot(data_1D[0],data_I)
+fig = ax.errorbar(data_1D[0],data_I,yerr=data_sig)
+ax.set_xscale('log')
+ax.set_yscale('log')
+ax.set_xlabel(r'$Q\/[\AA^{-1}]$',fontsize=25)
+ax.set_ylabel('intensity [a.u.]',fontsize=25)
+# ax.set_xticks([0.01,0.1,0.4,0.6])
+ax.get_xaxis().set_major_formatter(ticker.ScalarFormatter())
+ax.tick_params(labelsize=25)
+#plt.show()
+plt.savefig(args.sample+"_"+temperature+".png", bbox_inches="tight", dpi=600)
+
+data_out = np.column_stack((data_1D[0],data_I,data_sig))
+np.savetxt(args.sample+"_subtracted.dat",data_out,delimiter='\t',fmt='%s')