![]() Target that folder with the command listed above in (2). QP Script: Export images in a format that can be read by CellPose. Less important, but my current workflow is: This works within an Anaconda prompt while in the correct (with CellPose installed) virtual environment. Python -m cellpose -dir J:/CellPoseProcess/Treated/ -pretrained_model cyto -use_gpu -cellprob_threshold -4.0 flow_threshold 1.4 -diameter 17.9 -chan 0 -save_png -no_npy ![]() Run CellPose and batch process files with a command line like the following: The scripts work, and I have one that can copy a file from one location to another that works and can output text results to the QuPath log. How to call python script from Groovy and the python script in turn calls another python script - #6 by Mike_Nelson And maybe I shouldn’t be?Ĭall general Python scripts using the Windows command line from QuPath, as seen here: TLDR: QuPath scripts can call Python scripts, but I am unable to run a command line function in an Anaconda virtual environment from within a QuPath script. Goal: Use a command line function that works in an Anaconda virtual environment (to run CellPose on a batch of images) within QuPath/Groovy (Windows10). I am hoping I am missing something obvious, or the answer is “you can’t get there from here.” To install conda packages, you can create an environment through the ArcGIS Pro Package Manager or conda command line utilities.Hi all! This is something I have been struggling with for a little while, and I suspect it is due to my lack of familiarity with how software in different environments is supposed to interact. As of ArcGIS Pro 2.2, the default arcgispro-p圓 environment cannot be modified using the ArcGIS Pro Package Manager, even when running ArcGIS Pro with administrative privileges. From there, you can call arcgispro-p圓\python.exe by typing Python to start an interactive terminal session, or type python followed by the name of the script you want to run.Īre administrative privileges required to install conda packages? proenv.bat-Activates the ArcGIS Pro environment and opens a command prompt window.If you can call propy.bat without argument, the conda environment is activated, and Python is launched in interactive window mode (REPL).Activates the ArcGIS Pro conda environment.With a script as argument, propy.bat does the following:. ![]() You can call propy.bat with or without a Python file as an argument. It activates the ArcGIS Pro conda environment arcgispro-p圓 and launches Python.
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