Merge branch 'main' of https://github.com/mouseland/suite2p

README.md

@@ -91,7 +91,7 @@ The software has been heavily tested on Windows 10 and Ubuntu 18.04, and less we
 2. Run `conda env create --name suite2p`
 3. To activate this new environment, run `conda activate suite2p` (you will have to activate every time you want to run suite2p)
 4. Install the local version of suite2p into this environment in develop mode with the command `pip install -e .`
-5. Run tests: `python setup.py test` or `pytest tests\`, this will automatically download the test data into your `suite2p` folder in `data/test_data` (this download is 1.6GB and can be downloaded also from this [link](https://www.suite2p.org/static/test_data/test_data.zip)).
+5. Run tests: `python setup.py test` or `pytest tests\`, this will automatically download the test data into your `suite2p` folder. The test data is split into two parts: test inputs and expected test outputs which will be downloaded in `data/test_inputs` and `data/test_outputs` respectively. The .zip files for these two parts can be downloaded from these links: [test_inputs](https://www.suite2p.org/static/test_data/test_inputs.zip) and [test_outputs](https://www.suite2p.org/static/test_data/test_outputs.zip).
 
 ## Examples
 

conftest.py

@@ -7,6 +7,7 @@
 from tqdm import tqdm
 from pathlib import Path
 from urllib.request import urlopen
+from tenacity import retry
 
 @pytest.fixture()
 def data_dir():
@@ -55,6 +56,7 @@ def extract_zip(cached_file, url, data_path):
     with zipfile.ZipFile(cached_file,"r") as zip_ref:
         zip_ref.extractall(data_path)
 
+@retry
 def download_url_to_file(url, dst, progress=True):
     r"""Download object at the given URL to a local path.
             Thanks to torch, slightly modified

docs/installation.rst

@@ -1,54 +1,36 @@
 Installation
 ----------------
 
-Install an `Anaconda`_ distribution of Python -- Choose **Python 3.x**
-and your operating system. Note you might need to use an anaconda prompt
-if you did not add anaconda to the path.
-
-1. Download the suite2p repository from GitHub using Git:  ``git clone https://github.com/MouseLand/suite2p``
-2. Open an anaconda prompt / command prompt with ``conda`` for **python
-   3** in the path
-3. Change the current directory to the suite2p folder: ``cd suite2p``
-4. Run ``conda env create -f environment.yml``
-5. To activate this new environment, run ``conda activate suite2p``. Afterwards, You should see ``(suite2p)`` on the left side of the terminal line.
-6. Install suite2p into this environment: ``pip install suite2p``
-7. Now run ``suite2p`` and you're all set.
-
-If you have an older ``suite2p`` environment you can remove it with
-``conda env remove -n suite2p`` before creating a new one.
-
-Note you will always have to run **conda activate suite2p** before you
-run suite2p. Conda ensures mkl_fft and numba run correctly and quickly
-on your machine. If you want to run jupyter notebooks in this
-environment, then also ``conda install jupyter``.
-
-To upgrade suite2p (package `here`_), run the following in the
-environment:
-
-::
-
-   pip install suite2p --upgrade
+Please refer to the suite2p `README`_ for the latest up-to-date installation instructions.
 
 **Common issues**
 
-If when running ``suite2p``, you receive the error:
-``No module named PyQt5.sip``, then try uninstalling and reinstalling
-pyqt5
+- If when running ``suite2p``, you receive the error:
+  ``No module named PyQt5.sip``, then try uninstalling and reinstalling pyqt5
+
+   ::
+
+      pip uninstall pyqt5 pyqt5-tools
+      pip install suite2p
 
-::
+- If when running ``suite2p``, you receive an error associated
+  with **matplotlib**, try upgrading it:
 
-   pip uninstall pyqt5 pyqt5-tools
-   pip install suite2p
+   ::
 
-If when running ``suite2p``, you receive an error associated
-with **matplotlib**, try upgrading it:
+      pip install matplotlib --upgrade
 
-::
+- If you are on Yosemite Mac OS, PyQt doesn't work, and you won't be able to install suite2p. More recent versions of Mac OS are fine.
 
-   pip install matplotlib --upgrade
+- If you are using Ubuntu 22.04 and run into the following issue:
 
-If you are on Yosemite Mac OS, PyQt doesn't work, and you won't be able
-to install suite2p. More recent versions of Mac OS are fine.
+  ::
+  
+     qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in even though it was found. 
+     This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application
+     may fix this problem.
+  
+  Follow this `link`_ to install Qt5 and the issue above should be fixed.
 
 The software has been heavily tested on Windows 10 and Ubuntu 18.04, and
 less well tested on Mac OS. Please post an issue if you have
@@ -84,3 +66,5 @@ Dependencies
 .. _matplotlib: https://matplotlib.org/
 .. _Anaconda: https://www.anaconda.com/download/
 .. _here: https://pypi.org/project/suite2p/
+.. _link: https://askubuntu.com/questions/1406379/qt5-install-problem-ubuntustudio-22-04/1406503#1406503
+.. _README: https://github.com/MouseLand/suite2p#readme

docs/registration.rst

@@ -50,7 +50,7 @@ Registering the frames to the reference image
 
 Once the reference image is obtained, we align each frame to the
 reference image. The frames are registered in batches of size
-``ops['batch_size']`` (default is 200 frames per batch).
+``ops['batch_size']`` (default is 500 frames per batch).
 
 We first perform rigid registration (assuming that the whole image
 shifts by some (dy,dx)), and then optionally after that we perform

docs/settings.rst

@@ -84,7 +84,7 @@ Registration
 - **nimg_init**: (*int, default: 200*) how many frames to use to
   compute reference image for registration
 
-- **batch_size**: (*int, default: 200*) how many frames to register
+- **batch_size**: (*int, default: 500*) how many frames to register
   simultaneously in each batch. This depends on memory constraints - it
   will be faster to run if the batch is larger, but it will require
   more RAM.

setup.py

@@ -29,6 +29,7 @@
       ]
 test_deps = [
       'pytest',
+      'tenacity',
       'tqdm',
       'pytest-qt==3.3.0',
     ]

suite2p/detection/chan2detect.py

@@ -73,14 +73,14 @@ def cellpose_overlap(stats, mimg2):
     from . import anatomical 
     masks = anatomical.roi_detect(mimg2)[0]
     Ly, Lx = masks.shape
-    redstats = np.zeros(len(stats), np.float32)
+    redstats = np.zeros((len(stats),2), np.float32) #changed the size of preallocated space
     for i in range(len(stats)):
         smask = np.zeros((Ly, Lx), np.uint16)
         ypix0, xpix0= stats[i]['ypix'], stats[i]['xpix']
         smask[ypix0, xpix0] = 1
         ious = utils.mask_ious(masks, smask)[0]
         iou = ious.max()
-        redstats[i] = np.array([iou>0.5, iou])
+        redstats[i,] = np.array([iou>0.5, iou]) #this had the wrong dimension
     return redstats
 
 def detect(ops, stats):