README.md

PDZ Extractor: GUI for pdz-tool

User interface for pdz-tool which converts Bruker XRF* spectral data PDZ files to open CSV and JPEG formats.

*Tested on PDZ files from Bruker Tracer 5i Handheld XRF.

Download and run

You can download and run PDZ Extractor as a Windows executable or directly with Python.

Windows executable

For Windows, PDZ Extractor is available as a portable executable that runs directly by double-clicking or running from the command prompt. No installation is required.

Here's how:

1. Download the latest Windows version under pdz-extractor_vx.y.z_win64_portable.exe.zip

2. Extract pdz-extractor_vx.y.z_win64_portable.exe from the ZIP.

3. Double-click the extracted pdz-extractor_vx.y.z_win64_portable.exe.

4. Wait up to 30 seconds for PDZ Extractor to open.

Note

Windows Defender SmartScreen might block you from running the executable via double-click:

• If you have admin privileges, try Option 1.
• If you have no admin privileges, try Option 2.

Why is it unrecognized and blocked? In short, it’s because this executable has no certificate. If an executable's certificate isn't found by Windows when double-clicked, Windows will block it from immediately running.

Run option 1: With admin privileges

If you have admin privileges:

1. Double-click on pdz-extractor_vx.y.z_win64_portable.exe.
2. On the Windows Defender SmartScreen pop-up, select More info.
3. Select Run anyway. No Run anyway? Select Don't run and try Option 2.
4. Wait for PDZ Extractor to open. This may take a few seconds.

Run option 2: Without admin privileges

If double-clicking the executable doesn’t work, try running it via the command prompt.

Not possible? You can try running on a virtual machine or contacting your machine admin.

You can find various ways online on how to run an executable via the command prompt, but I prefer these steps:

1. Copy the path of the executable:

   • Right-click the file. (On Windows 10, press and hold the Shift key and then right-click the file.)
   • Select Copy as path.

2. Open the Start menu (⊞ Win).

3. Type cmd.

4. Press the Enter key or select the Command Prompt app.

5. Paste into the prompt the executable path you copied with Ctrl·V.

6. Run by pressing Enter.

7. Wait for the executable to load. This may take a few seconds.

macOS app

For macOS, there is currently no app file available for PDZ Extractor.

Developers

PDZ Extractor runs on Python 3.11 with just a couple dependencies.

Dependencies

• pdz-tool
• python>=3.11
• tk
• pyinstaller<6 if you need to create executables or packages (6.y.z versions of pyinstaller can throw a error when closing the window on Windows)

Virtual environments

conda

If you use conda (Anaconda), it can be faster to manually create the environment instead of solving from environment.yml.

Change directory to the repo root and run these commands to manually create the environment in ./env:

conda create -y --prefix ./env python=3.11 --force
conda activate ./env
pip install pdz-tool
pip install "pyinstaller<6"

To activate the environment in the future, change directory to repo root and run conda activate ./env.

Creating portable executable and package

Run PyInstaller with the following arguments while in the source code directory.

For Windows:

pyinstaller --onefile --windowed --icon=icon.ico --add-data=C:\absolute\path\to\source\icon.ico;. main.py

For macOS:

pyinstaller --windowed --icon=icon.icns --add-data=\absolute\path\to\source\icon.icns;. main.py

The terminating ;. in the add-data path is necessary. The period . indicates the directory in which to add the data, here root. If the icons are moved to a subdirectory, this . will need to be replaced by that subdirectory path.

Credits

pdz-tool by Bruno Ducraux with extended features and fixes by Lars Maxfield

User interface created by Lars Maxfield

Image extraction adapted from read_pdz by Frank Ligterink

Icon by Good Stuff Non Sense, CC BY 4.0