Code Snippets#
Helpful snippets for all things LBM python.
Parameters#
:external+python:py:class:caiman.source_extraction.cnmf.params.CNMFParams
caiman.source_extraction.cnmf.params.CNMFParams
caiman.source_extraction.cnmf.params.CNMFParams
Napari on WSL#
sudo apt install x11-xserver-utils
import vispy
print(vispy.sys_info())
Pixi#
Install Pixi#
iwr -useb https://pixi.sh/install.ps1 | iex
curl -fsSL https://pixi.sh/install.sh | bash
Import conda environment#
pixi init --import ./environment.yml
Troubleshooting#
OpenCV#
Many imaging libraries that show image visualizations heavily rely on opencv, but don’t install it for you.
OpenCV has a plethora of external dependencies that should be installed with your system package manager:
Windows:
Scoop
Winget
Brew
Linux:
apt
Brew
conda
Linux Install Guide Windows Install Guide MacOS Install Guide (untested support)
You may need some additional dependencies on WSL2:
sudo apt-get update && apt-get install ffmpeg libsm6 libxext6 -y
Filepaths and data directories#
def get_files(pathnames: os.PathLike | List[os.PathLike | str]) -> List[PathLike[AnyStr]]:
"""
Expands a list of pathname patterns to form a sorted list of absolute filenames.
Parameters
----------
pathnames: os.PathLike
Pathname(s) or pathname pattern(s) to read.
Returns
-------
List[PathLike[AnyStr]]
List of absolute filenames.
"""
pathnames = Path(pathnames).expanduser() # expand ~ to /home/user
if not pathnames.exists():
raise FileNotFoundError(f'Path {pathnames} does not exist as a file or directory.')
if pathnames.is_file():
return [pathnames]
if pathnames.is_dir():
pathnames = [fpath for fpath in pathnames.glob("*.tif*")] # matches .tif and .tiff
return sorted(pathnames, key=path.basename)
ImportError: attempted relative import with no known parent package#
This almost always occurs when you try to run a specific script directly without running the python package i.e. python -m path/to/project/ vs python path/to/project/file.py
main python file
The purpose of this file is to tell our python package how to run the code.
You can execute main.py as if it were a python module, fixing the above import errors.
Like so:
`python /home/mbo/repos/scanreader/scanreader/__main__.py`
Equivlent to:
`python -m /home/mbo/repos/scanreader/scanreader/`
System Information#
cloudmesh-cmd5 is a helpful library to view system information.
Install via pip:
pip install cloudmesh-sys
Attribute |
Value |
|---|---|
BUG_REPORT_URL |
“https://bugs.launchpad.net/ubuntu/” |
DISTRIB_CODENAME |
jammy |
DISTRIB_DESCRIPTION |
“Ubuntu 22.04.4 LTS” |
DISTRIB_ID |
Ubuntu |
DISTRIB_RELEASE |
22.04 |
HOME_URL |
“https://www.ubuntu.com/” |
ID |
ubuntu |
ID_LIKE |
debian |
NAME |
“Ubuntu” |
PRETTY_NAME |
“Ubuntu 22.04.4 LTS” |
PRIVACY_POLICY_URL |
“https://www.ubuntu.com/legal/terms-and-policies/privacy-policy” |
SUPPORT_URL |
“https://help.ubuntu.com/” |
UBUNTU_CODENAME |
jammy |
VERSION |
“22.04.4 LTS (Jammy Jellyfish)” |
VERSION_CODENAME |
jammy |
VERSION_ID |
“22.04” |
cpu |
13th Gen Intel(R) Core(TM) i9-13900KS |
cpu_cores |
16 |
cpu_count |
32 |
cpu_threads |
32 |
date |
2024-08-15 15:59:58.462764 |
frequency |
scpufreq(current=3187.198999999998, min=0.0, max=0.0) |
mem.active |
248.8 MiB |
mem.available |
56.3 GiB |
mem.free |
55.7 GiB |
mem.inactive |
5.8 GiB |
mem.percent |
10.2 % |
mem.total |
62.7 GiB |
mem.used |
5.7 GiB |
platform.version |
#1 SMP Thu Mar 7 03:22:57 UTC 2024 |
python |
3.11.9 |
python.pip |
24.2 |
python.version |
3.11.9 |
sys.platform |
linux |
uname.machine |
x86_64 |
uname.node |
RBO-C2 |
uname.processor |
x86_64 |
uname.release |
5.15.150.1-microsoft-standard-WSL2 |
uname.system |
Linux |
uname.version |
#1 SMP Thu Mar 7 03:22:57 UTC 2024 |
user |
mbo |
+———————+——————————————————————————-+ |
Same package, Error on conda-forge only#
(base)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ conda activate mescore
(mescore)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ conda list | grep free
freetype 2.12.1 h267a509_2 conda-forge
freetype-py 2.4.0 pyhd8ed1ab_0 conda-forge
(mescore)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ conda activate mestest
(mestest)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ conda list | grep free
freeglut 3.2.2 ha6d2627_3 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
freetype-py 2.4.0 pypi_0 pypi
(mestest)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
(mestest)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ conda list | grep fast
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
fastplotlib 0.1.0a16 pypi_0 pypi
python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge
(mestest)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ conda activate mescore
(mescore)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ conda list | grep free
freeglut 3.2.2 ha6d2627_3 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
freetype-py 2.4.0 pyhd8ed1ab_0 conda-forge
(mescore)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ conda list | grep fast
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
fastplotlib 0.1.0a16 pypi_0 pypi
python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge
(mescore)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ conda list | grep mes
# packages in environment at /home/mbo/miniconda3/envs/mescore:
cloudmesh-cmd5 5.0.20 pypi_0 pypi
cloudmesh-common 5.0.60 pypi_0 pypi
mesmerize-core 0.4.0 pyhd8ed1ab_0 conda-forge
mesmerize-viz 0.1.0 pypi_0 pypi
(mescore)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ ipython
Python 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.26.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: import freetype
In [2]: freetype.GlyphSlot
Out[2]: freetype.GlyphSlot
In [3]: freetype.GlyphSlot.render
Out[3]: <function freetype.GlyphSlot.render(self, render_mode)>
In [4]: exit
(mescore)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ conda activate mestest
(mestest)
mbo at RBO-C2 in ~/repos/LBM-CaImAn-Python (pixi●●)
$ ipython
In [1]: import freetype
In [2]: freetype.GlyphSlot.render
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[3], line 1
----> 1 freetype.GlyphSlot.render
AttributeError: type object 'GlyphSlot' has no attribute 'render'
FAQ#
1. Foreward slash or backwards slash#
When in doubt, use a / foreward slash.
This will work for windows C:/Users/ without needing a double backslash using `pathlib.Path() (built into python).
This will automatically return you a Windows Path or a PosixPath.
Filepaths on WSL
Be sure to not confuse your wsl path //$wsl/home/MBO with your windows home path C:/Users/MBO.
# this works on any operating system, any filepath structure
data_path = Path().home() / 'Documents' / 'data' / 'high_res'
raw_files = [x for x in data_path.glob(f'*.tif*')]