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.. note:: Note that the GUI is currently not supported on Python>=3.12.
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This command will process ``"SiO2 uncorrected.xy"``,
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all files in the ``input_dir`` directory, all files listed in ``file_list.txt``,
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all ``.chi`` files in the current directory, and all files matching the pattern ``data``,
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using a muD value of 2.5.
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Check ``labpdfproc --help`` to see all supported file types.
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This will open the GUI, which should look something like,
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In the GUI, you can select multiple individual files via the file browser, but not entire directories.
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To include directories, you can either:
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(1) create a text file named ``file_list.txt`` containing the desired paths and load it,
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(2) manually select all files in a folder, or
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(3) enter paths manually separated by a colon with no spaces.
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.. image:: ../img/labpdfproc-gui.jpeg
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:align:center
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We will now continue using ``zro2_mo.xy`` as the example input throughout the rest of this tutorial.
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Below we will go through all the commands using the CLI, but the same principles apply to the GUI.
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.. note:: The first time you run any of the below commands,
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you will be prompted to enter your name, email, and ORCID. This will be
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appended to metadata in the output file header for reproducibility and tracking purposes.
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4. The muD value is required for absorption correction, and you can specify it in one of the four ways:
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.. code-block:: python
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``labpdfproc mud`` Command
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---------------------------
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# Option 1: Manual value
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labpdfproc zro2_mo.xy --mud 2.5
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# Option 2: From a z-scan file
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labpdfproc zro2_mo.xy -z zscan.xy
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# Option 3: Using sample mass density
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labpdfproc zro2_mo.xy -d ZrO2,17.45,1.2
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# Option 4: Using packing fraction
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labpdfproc zro2_mo.xy -p ZrO2,17.45,0.2
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If you know the muD value for your sample, you can use the ``labpdfproc mud``
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command to apply absorption correction directly.
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Note that you can only use one method at a time. The following examples are not allowed:
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To see all the options for this command, type,
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.. code-block:: python
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.. code-block:: bash
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labpdfproc zro2_mo.xy --mud 2.5-z zscan.xy
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labpdfproc zro2_mo.xy --mud 2.5-d ZrO2,17.45,1.2
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labpdfproc mud -h
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If the packing fraction option is not supported at the moment, you can approximate the sample mass density as:
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``mass density = packing fraction * material density``, where the material density can be looked up manually.
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To run the correction, specify the path to your diffraction data file(s) and the muD value,
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.. code-block:: bash
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5. You can specify the wavelength in two ways:
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labpdfproc mud <diffraction-data-file.xy><mud>
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labpdfproc mud zro2_mo.xy 2.5
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.. code-block:: python
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If the flag ``--wavelength`` is not specified, the program will attempt to fetch
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the wavelength from a configuration file.
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If the wavelength is not found in the configuration file, a ``ValueError``
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will be raised, prompting you to provide the wavelength either through the CLI or the configuration file.
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# Option 1: Manually enter wavelength
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labpdfproc zro2_mo.xy --mud 2.5-w 0.71303
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# Option 2: Use a known anode type
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labpdfproc zro2_mo.xy --mud 2.5-a Mo
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To provide the wavelength through the CLI, you can use the ``-w`` or ``--wavelength`` flag followed by the wavelength value in angstroms or the X-ray source.
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For example,
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Do not use both ``-w`` and ``-a`` at the same time. For example:
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.. code-block:: bash
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.. code-block:: python
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labpdfproc mud zro2_mo.xy 2.5 -w 0.71303
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labpdfproc mud zro2_mo.xy 2.5 -w Mo
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labpdfproc zro2_mo.xy --mud 2.5-w 0.71303-a Mo
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This will then save the corrected file in the same directory as the input file with the name ``zro2_mo_corrected.chi``.
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is not valid. This is to avoid confusion when wavelength conflicts with anode type.
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To avoid retyping, you can save your wavelength or anode type in a diffpy configuration file.
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See full instructions at https://www.diffpy.org/diffpy.labpdfproc/examples/tools_example.html.
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To save the correction file, specify the ``-c`` or ``--output-correction`` flag,
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.. code-block:: bash
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6. You are also encouraged to provide your information (name, email, and orcid) for reproducibility:
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labpdfproc mud zro2_mo.xy 2.5 -w 0.71303 -c
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.. code-block:: python
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This will then save the correction file in the same directory as the input file with the name ``zro2_mo_cve.chi``.
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labpdfproc zro2_mo.xy --mud 2.5-n Joe -e Joe@email.com --orcid 0000-0000-0000-0000
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``labpdfproc zscan`` Command
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----------------------------
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The ``labpdfproc zscan`` command allows you to calculate the muD value from a z-scan file and apply absorption correction to your diffraction data.
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For more information on what a z-scan is, please see the "Examples --> Linear Absorption Coefficient Examples"
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section in the ``diffpy.utils`` documentation: https://www.diffpy.org/diffpy.utils/examples/mu_calc_examples.html.
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Alternatively, you can enter this information during the interactive prompts
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or save it in your diffpy configuration file.
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For more details, refer to https://www.diffpy.org/diffpy.utils/examples/tools_example.html.
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To see the options for this command, type,
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.. code-block:: bash
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7. You can further customize the diffraction correction process using the following options:
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labpdfproc zscan -h
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- Choose xtype: use ``-x`` to specify your input data's xtype, which will be used for the output.
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- Select correction method: use ``-m`` to choose between "brute_force" or "polynomial_interpolation" (faster and preferred for muD 0.5-7).
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- Specify output directory: use ``-o`` to save the corrected file(s) to a specific folder.
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- Add custom metadata: use ``-u`` to provide key-value pair for information tracking (e.g., experimental details).
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- Output the cve file: use ``-c`` to export the cve file along with the corrected data.
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- Overwrite existing files: use ``-f`` to replace any previous corrected files with the same names.
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To run this command, provide the path to your diffraction data file(s) and the z-scan file,
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.. code-block:: bash
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8. To summarize, a full command might look like this:
This will then save the correction file in the same directory as the input file with the name ``CeO2_635um_accum_0_cve.chi``.
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``labpdfproc sample`` Command
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-----------------------------
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The ``labpdfproc sample`` command allows you to calculate the muD value from information
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about your sample and apply absorption correction to your diffraction data.
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To see the options for this command, type,
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.. code-block:: bash
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labpdfproc sample -h
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To run this command, provide the path to your diffraction data file(s) along with:
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1) ``sample_composition``: The chemical formula of your sample.
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2) ``sample_mass_density``: The mass density of your sample in g/cm^3. If you don't know the mass density, a good approximation is typically ~1/3 of the theoretical packing fraction.
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3) ``diameter``: The outer diameter of your capillary.
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