"\u001b[0;32m<ipython-input-2-f7378930c369>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 13\u001b[0m \u001b[0mspobj\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mfsldir\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;34m'/bin/fslstats'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutfile\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'-V'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstdout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mPIPE\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0msout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mspobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstdout\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'utf-8'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 15\u001b[0;31m \u001b[0mvol_vox\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msout\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 16\u001b[0m \u001b[0mvol_mm\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msout\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 17\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Volumes are: '\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvol_vox\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m' in voxels and '\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvol_mm\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m' in mm'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mIndexError\u001b[0m: list index out of range"
],
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"#!/usr/bin/env fslpython\n",
"import os, sys\n",
...
...
@@ -272,55 +235,9 @@
"vol_mm = float(sout.split()[1])\n",
"print('Volumes are: ', vol_vox, ' in voxels and ', vol_mm, ' in mm')"
]
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%% Cell type:markdown id: tags:
# Callable scripts in python
In this tutorial we will cover how to write simple stand-alone scripts in python that can be used as alternatives to bash scripts.
There are some code blocks within this webpage, but we recommend that you write the code in an IDE or editor instead and then run the scripts from a terminal.
## Basic script
The first line of a python script is usually:
%% Cell type:code id: tags:
```python
```
#!/usr/bin/env python
```
%% Cell type:markdown id: tags:
which invokes whichever version of python can be found by `/usr/bin/env` since python can be located in many different places.
For FSL scripts we use an alternative, to ensure that we pick up the version of python (and associated packages) that we ship with FSL. To do this we use the line:
%% Cell type:code id: tags:
```python
```
#!/usr/bin/env fslpython
```
%% Cell type:markdown id: tags:
After this line the rest of the file just uses regular python syntax, as in the other tutorials. Make sure you make the file executable - just like a bash script.
## Calling other executables
The most essential call that you need to use to replicate the way a bash script calls executables is `subprocess.run()`. A simple call looks like this:
> Note that the `decode` call in the middle line converts the string from a byte string to a normal string. In Python 3 there is a distinction between strings (sequences of characters, possibly using multiple bytes to store each character) and bytes (sequences of bytes). The world has moved on from ASCII, so in this day and age, this distinction is absolutely necessary, and Python does a fairly good job of it.
If the output is numerical then this can be extracted like this:
if cmd: # avoids empty strings getting passed to sp.run()
print('Running command: ', cmd)
spobj = sp.run(cmd.split(), stdout = sp.PIPE)
sout.append(spobj.stdout.decode('utf-8'))
```
%% Cell type:markdown id: tags:
## Command line arguments
The simplest way of dealing with command line arguments is use the module `sys`, which gives access to an `argv` list:
%% Cell type:code id: tags:
```python
```
import sys
print(len(sys.argv))
print(sys.argv[0])
```
%% Cell type:markdown id: tags:
For more sophisticated argument parsing you can use `argparse` - good documentation and examples of this can be found on the web.
## Example script
Here is a simple bash script (it masks an image and calculates volumes - just as a random example). DO NOT execute the code blocks here within the notebook/webpage:
