xrdPlanner 2.4.2__tar.gz → 2.5.3__tar.gz

{xrdplanner-2.4.2 → xrdplanner-2.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xrdPlanner
-Version: 2.4.2
+Version: 2.5.3
 Summary: A tool to project X-ray diffraction cones on a detector screen at different geometries (tilt, rotation, offset) and X-ray energies
 Author-email: Lennard Krause <lkrause@chem.au.dk>
 Project-URL: Homepage, https://github.com/LennardKrause/xrdPlanner
@@ -18,11 +18,11 @@ Requires-Dist: numpy>=1.24
 Requires-Dist: pyqtgraph>=0.13
 Requires-Dist: Dans_Diffraction>=2.2.3
 Requires-Dist: PyQt6>=6.5
-Requires-Dist: pyFAI>=2023.5
+Requires-Dist: xraydb>=4.5.8
 Dynamic: license-file
 
 # xrdPlanner
-## Version 2.4.1 (released 05.03.2025)
+## Version 2.5.3 (released 15.10.2026)
 #### A tool to project X-ray diffraction cones on a detector screen at different geometries (tilt, rotation, offset) and X-ray energies
  - Article published in [_J. Synchrotron Rad._ (2024). **31**](https://doi.org/10.1107/S1600577523011086).
  - Main application is to visualize the maximum achievable resolution at a given geometry.
@@ -34,7 +34,7 @@ Dynamic: license-file
  - The math used is not meant to bring people to the moon but to provide a quick and simple preview.
  - This is not meant to accurately simulate a diffraction experiment, the step sizes are integer values in mm or degrees.
  - The module building code is designed for [Dectris](https://www.dectris.com) [PILATUS3](https://www.dectris.com/detectors/x-ray-detectors/pilatus3/) / [EIGER2](https://www.dectris.com/detectors/x-ray-detectors/eiger2/) or [SACLA](https://sacla.xfel.jp/?lang=en) MPCCD Detectors (central hole geometry) but one-module systems like the [Bruker](https://www.bruker.com/en.html) [Photon II](https://www.bruker.com/en/products-and-solutions/diffractometers-and-scattering-systems/single-crystal-x-ray-diffractometers/sc-xrd-components/detectors.html) and [Rayonix](https://www.rayonix.com/) [MX-HS](https://www.rayonix.com/rayonix-mx-hs-series/) are possible as well.
- - It uses [python3](https://www.python.org), [numpy](https://numpy.org), [pyqt6](https://www.riverbankcomputing.com/software/pyqt/), [pyqtgraph](https://pyqtgraph.readthedocs.io/en/latest/), [pyFAI](https://pyfai.readthedocs.io/en/v2023.1/) and [Dans_Diffraction](https://github.com/DanPorter/Dans_Diffraction).
+ - It uses [python3](https://www.python.org), [numpy](https://numpy.org), [pyqt6](https://www.riverbankcomputing.com/software/pyqt/), [pyqtgraph](https://pyqtgraph.readthedocs.io/en/latest/), [xraydb](https://github.com/xraypy/XrayDB), [Dans_Diffraction](https://github.com/DanPorter/Dans_Diffraction) and [pyFAI](https://pyfai.readthedocs.io/en/v2023.1/) (optional).
 
 >[!TIP]
 >## Short how-to:
@@ -42,13 +42,15 @@ Dynamic: license-file
 > - Type _xrdPlanner_ in a terminal and hit enter.
 > - Choose a detector and a model from the _Detector_ menu.
 > - Plot diffraction cone contours:
->   - Pick a reference from the _Reference_ menu ([pyFAI](https://pyfai.readthedocs.io/en/v2023.1/)), no hkl tooltip available.
+>   - Pick a reference from the _Reference_ menu ([pyFAI](https://pyfai.readthedocs.io/en/v2023.1/)), if available.
 >   - Drop a .cif file onto the window ([Dans_Diffraction](https://github.com/DanPorter/Dans_Diffraction)), click a contour to get a hkl tooltip.
 >   - Enter custom unit cell dimensions, click a contour to get a hkl tooltip.
 > - Use the units from the _Units_ menu you are the most comfortable with.
 > - Hover over the grey line at the top to show the sliders. Click it to make it stay open.
 > - Drag the sliders to change energy and geometry.
 > - Use [hotkeys](#hotkeys) to streamline your experience.
+> - Check out the [PXRD plot window](#pxrd-pattern-plot) and set the [intrumental peak broadening](#instrumental-broadening).
+> - Have a look at the [absorption](#absorption-transmission-and-fluorescence) spectrum of the sample and check the fluorescence.
 >
 >## Customisation:
 >  - Use the [export window](#export-window) from the settings menu.
@@ -66,6 +68,9 @@ Dynamic: license-file
 >    - Download a settings file from here (e.g. settings/DanMAX.json).
 >    - Use the import settings function from the GUI to import.
 
+>[!NOTE]
+> - Set the environmental variable 'XRDPLANNER' to specify the settings file directory.
+
 ## Conventions
 The geometry is defined with the center of rotation at the sample position, such that the radius of the rotation circle is equal to the sample to detector distance (SDD). That is, the rotation moves the detector along the goniometer circle, keeping the point of normal incidence (PONI) at the same position relative to the detector surface. At 0° the detector is vertical and at 90° the detector is horizontal with the detector normal pointing down.
 The tilt angle is defined relative to the detector face and such that the PONI shifts along the detector face, keeping the SDD fixed. The detector face is thus always tangential to the goniometer circle. The $tilt$ can intuitively be described as a rolling motion along the goniometer circle and is considered a convenience function as it is equivalent to a combination of $rotation$ and $y_{offset}$. Consequently, the vertical shift of the PONI position ($\Delta y_{PONI}$) on the detector face is equal to the arclength of a section on the goniometer circle with an angular span equal to the tilt angle.
@@ -111,17 +116,19 @@ S_{ij} = \left(\frac{|\vec{v}_{ij}|}{SDD}\right)^{-3}
 ```
 where $SDD$ is the sample to detector distance.
 
->[!NOTE]
->## Update to Version 2.0.0 and later (released 23.09.2024)
-> - The definition of detector modules was changed from mm to px to be more accurate and consistent.
-> - Consequently, custom detectors added to the detector_db file pre 2.0.0 are no longer working.
-> - A new [detector db editor](#detector-db-editor) was added (_Settings_ > _Detector db editor_) to make the addition of custom detectors more feasible.
-> - Define and add whatever detector you collect your data with, now more easily.
-> - If something goes wrong use _Settings_ > _Reset detector db_.
-> - There is a backup of your _custom_ detector_db (detector_db.json.bak) in the xrdPlanner folder (_Help_ > _xrdPlanner_).
-> - A new parameter was added to allow for detector screen padding (plo.plot_padding), default is 0.
-
 ## Latest updates:
+  - 2026-10-15 Bugfix: Fixed a bug on windows to get the username.
+  - 2026-10-15 Update: Change the way references are handled internally.
+  - 2026-10-13 Update: Added a new limit variable to determine the detector energy threshold settings (PILATUS, EIGER, ...).
+  - 2026-10-13 Bugfix: Fixed a bug in the variable range startup check.
+  - 2026-10-12 Update: Added a correction factor to calculate the instrumental FWHM (effective sample diameter).
+  - 2026-10-12 Update: Added the environmental variable 'XRDPLANNER' to specify the settings file directory.
+  - 2026-10-12 Update: Added the effective sample to detector distance (D) to the hover overlay. 
+  - 2026-10-12 Update: Added a new window to show the [absorption](#absorption-transmission-and-fluorescence) spectrum of the cif file (requires xraydb).
+  - 2026-10-12 Update: pyFAI is now optional (calibrants are only available if pyFAI is installed).
+  - 2025-04-01 Update: Settings files (.json) can now be dropped on the window.
+  - 2025-04-01 Update: The pxrd ghosts stay a little longer now.
+  - 2025-04-01 Update: Added the option to set the environmental variable 'XRDPLANNER' to specify the xrdPlanner home path.
   - 2025-03-05 Update: The slider values now accept input (thanks Clemens and Guðrún).
   - 2025-03-05 Bugfix: Windows that allow typing will now disregard hotkeys.
   - 2025-03-04 Update: Allowed smaller pixels in the detector-db editor (thanks tjalb).
@@ -241,12 +248,17 @@ where $SDD$ is the sample to detector distance.
  - Estimated beam divergence
  - Expected bandwidth of the incident X-ray beam
  - Intersection of the sample size and the beam size as the diameter
+ - Added a correction factor of 2/3 to the sample diameter to reflect the average distance from any point on a disc to the center of the disc.
 
 > **The interested user is referred to the article:<br>**
 >  <i>On the resolution function for powder diffraction with area detectors</i><br>
 >  [D. Chernyshov <i> et al., Acta Cryst.</i> (2021). <b>A77</b>, 497-505](https://doi.org/10.1107/S2053273321007506)
 <img src="https://github.com/LennardKrause/xrdPlanner/blob/main/examples/Figure_6_FWHM.png" width="50%">
 
+#### Absorption, transmission and fluorescence
+##### Display the X-ray absorption spectra and analyse the sample transmission and fluorescence emission bands of the current cif file.
+<img src="https://github.com/LennardKrause/xrdPlanner/blob/main/examples/Figure_7_Abs.png" width="50%">
+
 ## Hotkeys
 
 | Key        | Action                    |
@@ -255,6 +267,7 @@ where $SDD$ is the sample to detector distance.
 | F2         | Show Geometry conventions |
 | F3         | Show Hotkeys              |
 | x          | Show PXRD pattern         |
+| b          | Show Absorption window    |
 | f          | Show FWHM window          |
 | #          | *Display units*           |
 | t          | 2-Theta                   |
@@ -453,6 +466,8 @@ where $SDD$ is the sample to detector distance.
     bsdx_min = 5     # [int] Beamstop distance minimum [mm]
     bsdx_max = 1000  # [int] Beamstop distance maximum [mm]
     bsdx_stp = 1     # [int] Beamstop distance step size [mm]
+    
+    det_thrs = 0.5   # [float] Detector threshold [frac]
 
 </details>
 

{xrdplanner-2.4.2 → xrdplanner-2.5.3}/README.md

@@ -1,5 +1,5 @@
 # xrdPlanner
-## Version 2.4.1 (released 05.03.2025)
+## Version 2.5.3 (released 15.10.2026)
 #### A tool to project X-ray diffraction cones on a detector screen at different geometries (tilt, rotation, offset) and X-ray energies
  - Article published in [_J. Synchrotron Rad._ (2024). **31**](https://doi.org/10.1107/S1600577523011086).
  - Main application is to visualize the maximum achievable resolution at a given geometry.
@@ -11,7 +11,7 @@
  - The math used is not meant to bring people to the moon but to provide a quick and simple preview.
  - This is not meant to accurately simulate a diffraction experiment, the step sizes are integer values in mm or degrees.
  - The module building code is designed for [Dectris](https://www.dectris.com) [PILATUS3](https://www.dectris.com/detectors/x-ray-detectors/pilatus3/) / [EIGER2](https://www.dectris.com/detectors/x-ray-detectors/eiger2/) or [SACLA](https://sacla.xfel.jp/?lang=en) MPCCD Detectors (central hole geometry) but one-module systems like the [Bruker](https://www.bruker.com/en.html) [Photon II](https://www.bruker.com/en/products-and-solutions/diffractometers-and-scattering-systems/single-crystal-x-ray-diffractometers/sc-xrd-components/detectors.html) and [Rayonix](https://www.rayonix.com/) [MX-HS](https://www.rayonix.com/rayonix-mx-hs-series/) are possible as well.
- - It uses [python3](https://www.python.org), [numpy](https://numpy.org), [pyqt6](https://www.riverbankcomputing.com/software/pyqt/), [pyqtgraph](https://pyqtgraph.readthedocs.io/en/latest/), [pyFAI](https://pyfai.readthedocs.io/en/v2023.1/) and [Dans_Diffraction](https://github.com/DanPorter/Dans_Diffraction).
+ - It uses [python3](https://www.python.org), [numpy](https://numpy.org), [pyqt6](https://www.riverbankcomputing.com/software/pyqt/), [pyqtgraph](https://pyqtgraph.readthedocs.io/en/latest/), [xraydb](https://github.com/xraypy/XrayDB), [Dans_Diffraction](https://github.com/DanPorter/Dans_Diffraction) and [pyFAI](https://pyfai.readthedocs.io/en/v2023.1/) (optional).
 
 >[!TIP]
 >## Short how-to:
@@ -19,13 +19,15 @@
 > - Type _xrdPlanner_ in a terminal and hit enter.
 > - Choose a detector and a model from the _Detector_ menu.
 > - Plot diffraction cone contours:
->   - Pick a reference from the _Reference_ menu ([pyFAI](https://pyfai.readthedocs.io/en/v2023.1/)), no hkl tooltip available.
+>   - Pick a reference from the _Reference_ menu ([pyFAI](https://pyfai.readthedocs.io/en/v2023.1/)), if available.
 >   - Drop a .cif file onto the window ([Dans_Diffraction](https://github.com/DanPorter/Dans_Diffraction)), click a contour to get a hkl tooltip.
 >   - Enter custom unit cell dimensions, click a contour to get a hkl tooltip.
 > - Use the units from the _Units_ menu you are the most comfortable with.
 > - Hover over the grey line at the top to show the sliders. Click it to make it stay open.
 > - Drag the sliders to change energy and geometry.
 > - Use [hotkeys](#hotkeys) to streamline your experience.
+> - Check out the [PXRD plot window](#pxrd-pattern-plot) and set the [intrumental peak broadening](#instrumental-broadening).
+> - Have a look at the [absorption](#absorption-transmission-and-fluorescence) spectrum of the sample and check the fluorescence.
 >
 >## Customisation:
 >  - Use the [export window](#export-window) from the settings menu.
@@ -43,6 +45,9 @@
 >    - Download a settings file from here (e.g. settings/DanMAX.json).
 >    - Use the import settings function from the GUI to import.
 
+>[!NOTE]
+> - Set the environmental variable 'XRDPLANNER' to specify the settings file directory.
+
 ## Conventions
 The geometry is defined with the center of rotation at the sample position, such that the radius of the rotation circle is equal to the sample to detector distance (SDD). That is, the rotation moves the detector along the goniometer circle, keeping the point of normal incidence (PONI) at the same position relative to the detector surface. At 0° the detector is vertical and at 90° the detector is horizontal with the detector normal pointing down.
 The tilt angle is defined relative to the detector face and such that the PONI shifts along the detector face, keeping the SDD fixed. The detector face is thus always tangential to the goniometer circle. The $tilt$ can intuitively be described as a rolling motion along the goniometer circle and is considered a convenience function as it is equivalent to a combination of $rotation$ and $y_{offset}$. Consequently, the vertical shift of the PONI position ($\Delta y_{PONI}$) on the detector face is equal to the arclength of a section on the goniometer circle with an angular span equal to the tilt angle.
@@ -88,17 +93,19 @@ S_{ij} = \left(\frac{|\vec{v}_{ij}|}{SDD}\right)^{-3}
 ```
 where $SDD$ is the sample to detector distance.
 
->[!NOTE]
->## Update to Version 2.0.0 and later (released 23.09.2024)
-> - The definition of detector modules was changed from mm to px to be more accurate and consistent.
-> - Consequently, custom detectors added to the detector_db file pre 2.0.0 are no longer working.
-> - A new [detector db editor](#detector-db-editor) was added (_Settings_ > _Detector db editor_) to make the addition of custom detectors more feasible.
-> - Define and add whatever detector you collect your data with, now more easily.
-> - If something goes wrong use _Settings_ > _Reset detector db_.
-> - There is a backup of your _custom_ detector_db (detector_db.json.bak) in the xrdPlanner folder (_Help_ > _xrdPlanner_).
-> - A new parameter was added to allow for detector screen padding (plo.plot_padding), default is 0.
-
 ## Latest updates:
+  - 2026-10-15 Bugfix: Fixed a bug on windows to get the username.
+  - 2026-10-15 Update: Change the way references are handled internally.
+  - 2026-10-13 Update: Added a new limit variable to determine the detector energy threshold settings (PILATUS, EIGER, ...).
+  - 2026-10-13 Bugfix: Fixed a bug in the variable range startup check.
+  - 2026-10-12 Update: Added a correction factor to calculate the instrumental FWHM (effective sample diameter).
+  - 2026-10-12 Update: Added the environmental variable 'XRDPLANNER' to specify the settings file directory.
+  - 2026-10-12 Update: Added the effective sample to detector distance (D) to the hover overlay. 
+  - 2026-10-12 Update: Added a new window to show the [absorption](#absorption-transmission-and-fluorescence) spectrum of the cif file (requires xraydb).
+  - 2026-10-12 Update: pyFAI is now optional (calibrants are only available if pyFAI is installed).
+  - 2025-04-01 Update: Settings files (.json) can now be dropped on the window.
+  - 2025-04-01 Update: The pxrd ghosts stay a little longer now.
+  - 2025-04-01 Update: Added the option to set the environmental variable 'XRDPLANNER' to specify the xrdPlanner home path.
   - 2025-03-05 Update: The slider values now accept input (thanks Clemens and Guðrún).
   - 2025-03-05 Bugfix: Windows that allow typing will now disregard hotkeys.
   - 2025-03-04 Update: Allowed smaller pixels in the detector-db editor (thanks tjalb).
@@ -218,12 +225,17 @@ where $SDD$ is the sample to detector distance.
  - Estimated beam divergence
  - Expected bandwidth of the incident X-ray beam
  - Intersection of the sample size and the beam size as the diameter
+ - Added a correction factor of 2/3 to the sample diameter to reflect the average distance from any point on a disc to the center of the disc.
 
 > **The interested user is referred to the article:<br>**
 >  <i>On the resolution function for powder diffraction with area detectors</i><br>
 >  [D. Chernyshov <i> et al., Acta Cryst.</i> (2021). <b>A77</b>, 497-505](https://doi.org/10.1107/S2053273321007506)
 <img src="https://github.com/LennardKrause/xrdPlanner/blob/main/examples/Figure_6_FWHM.png" width="50%">
 
+#### Absorption, transmission and fluorescence
+##### Display the X-ray absorption spectra and analyse the sample transmission and fluorescence emission bands of the current cif file.
+<img src="https://github.com/LennardKrause/xrdPlanner/blob/main/examples/Figure_7_Abs.png" width="50%">
+
 ## Hotkeys
 
 | Key        | Action                    |
@@ -232,6 +244,7 @@ where $SDD$ is the sample to detector distance.
 | F2         | Show Geometry conventions |
 | F3         | Show Hotkeys              |
 | x          | Show PXRD pattern         |
+| b          | Show Absorption window    |
 | f          | Show FWHM window          |
 | #          | *Display units*           |
 | t          | 2-Theta                   |
@@ -430,6 +443,8 @@ where $SDD$ is the sample to detector distance.
     bsdx_min = 5     # [int] Beamstop distance minimum [mm]
     bsdx_max = 1000  # [int] Beamstop distance maximum [mm]
     bsdx_stp = 1     # [int] Beamstop distance step size [mm]
+    
+    det_thrs = 0.5   # [float] Detector threshold [frac]
 
 </details>
 

{xrdplanner-2.4.2 → xrdplanner-2.5.3}/pyproject.toml

@@ -11,7 +11,7 @@ dependencies = ["numpy >= 1.24",
                 "pyqtgraph >= 0.13",
                 "Dans_Diffraction >= 2.2.3",
                 "PyQt6 >= 6.5",
-                "pyFAI >= 2023.5",
+                "xraydb >= 4.5.8",
 ]
 classifiers = [
     "Programming Language :: Python :: 3",

{xrdplanner-2.4.2 → xrdplanner-2.5.3}/xrdPlanner/__init__.py

@@ -1,6 +1,6 @@
-__version__ = '2.4.2'
+__version__ = '2.5.3'
 __author__ = 'Lennard Krause'
 __authors__ = ['Lennard Krause', 'Frederik H. Gjørup', 'Mads R. V. Jørgensen']
 __email__ = 'lkrause@chem.au.dk'
-__date__ = '01.04.2025'
-__year__ = '2025'
+__date__ = '15.10.2026'
+__year__ = '2026'