Metadata-Version: 2.1
Name: btpytools
Version: 0.1.21
Summary: Helper functions for BakingTray and StitchIt
Home-page: https://github.com/SainsburyWellcomeCentre/btpytools
Author: Rob Campbell
Author-email: rob.campbell@ucl.ac.uk
License: UNKNOWN
Project-URL: Source Code, https://github.com/SainsburyWellcomeCentre/btpytools
Description: # StitchIt Python Tools
        
        The directory contains Python code for managing BakingTray serial-section 2p data.
        The main functions of interest are `compressRawData.py` and `transferToServer.py`, which are aimed at end users of the microscope. 
        The `recipe.py` and `tools.py` modules support these and are aimed at developers. 
        
        
        
        ## Install instructions
        ```
        $ sudo pip install btpytools
        
        ```
        
        Running as `sudo` allows the installer to add the most important programs to your path, allowing them to be run at the system command line:
        
        
        * `transferToServer`
        * `compressRawData`
        * `summariseAcqs`
        
        In other words, after pip installing you can run `compressRawData` at the command line. 
        
        ## Usage instructions
        
        ### Compressing the raw data directory
        `cd` to the sample directory at the command line and run `compressRawData`. This works much faster
        if you to have installed `lbzip2`, which runs parallel bzip. Likely only works on Linux. The
        command also confirms there is enough disk space available to complete successfully.
        
        ```
        $ cd /mnt/data/BakingTrayStacks/CC_125_1__125_2/ 
        $ compressRawData  
        ```
        
        ### Sending data to a remote server
        The server should be mounted locally to a mount point writable by the user. The tranfer is via `rsync`. The command just ensures no uncompressed raw data or uncropped stacks are copied. It brute-force retries if there is a failure for some reason. 
        
        First `cd` to the directory which **contains your samples**. Not the sample directory. e.g.
        ```
        $ cd /mnt/data/BakingTrayStacks
        ```
        
        You can now run in either of the following two ways (either one acquisition or multiple acquisitions)
        ```
        $ transferToServer RC_RabiesBrains01 /mnt/server/user/data/histology
        $ transferToServer RC_RabiesBrains01 RC_TwoProbeTracks_test RC_MyOldSample /mnt/server/user/data/histology
        ```
        
        Do **not** do the following as it will not send compressed raw data should you have any:
        ```
        $ transferToServer RC_RabiesBrains01/sample01 RC_RabiesBrains01/sample02 /mnt/server/user/data/histology
        ```
        
Platform: UNKNOWN
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: dev
