Merge branch 'dev'

Author: carsen-stringer

.travis.yml

@@ -1,4 +1,7 @@
 language: python
+dist: xenial
+services:
+  - xvfb
 jobs:
   include:
   - name: Python 3.7.1 on Linux
@@ -19,12 +22,25 @@ jobs:
     - bash ./miniconda.sh -b
     - export PATH=~/miniconda3/bin:$PATH
     - conda update --yes conda
+  - name: Python 3.7.7 on Windows
+    os: windows
+    language: shell
+    before_install:
+    - choco install python --version 3.7.7
+    - export MINICONDA=/c/miniconda
+    - MINICONDA_WIN=$(cygpath --windows $MINICONDA)
+    - choco install openssl.light
+    - choco install miniconda3 --params="'/AddToPath:0 /D:$MINICONDA_WIN'"
+    - PATH=$(echo "$PATH" | sed -e 's|:/c/ProgramData/chocolatey/bin||')
+    - PATH=$(echo "$PATH" | sed -e 's|:/c/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin||')
+    - source $MINICONDA/Scripts/activate
+    - source $MINICONDA/etc/profile.d/conda.sh
   allow_failures:
   - os: osx
 install:
 - conda env create -f environment.yml
 - source activate suite2p
-- pip install .[data]
+- pip install .[data,nwb]
 - dvc pull -r gdrive-travis
 - pip install coveralls
 script:

README.md

@@ -34,9 +34,10 @@ Install an [Anaconda](https://www.anaconda.com/download/) distribution of Python
 1. Download the [`environment.yml`](https://github.com/MouseLand/suite2p/blob/master/environment.yml) file from the repository. You can do this by cloning the repository, or copy-pasting the text from the file into a text document on your local computer.
 2. Open an anaconda prompt / command prompt with `conda` for **python 3** in the path
 3. Change directories to where the `environment.yml` is and run `conda env create -f environment.yml`
-4. Activate the environment with `conda activate suite2p'
+4. Activate the environment with `conda activate suite2p`
 5. Pip install suite2p into the environment: `pip install suite2p`
 6. Now run `suite2p` and you're all set.
+7. Running the command `suite2p --version` in the terminal will print the install version of suite2p.
 
 If you have an older `suite2p` environment you can remove it with `conda env remove -n suite2p` before creating a new one.
 

data/test_data.dvc

@@ -1,3 +1,3 @@
 outs:
-- md5: 484b58990efd6929863cd77108f68ab0.dir
+- md5: 273c132e8b2d31901a45c70188e68535.dir
   path: test_data

docs/deconvolution.rst

@@ -32,10 +32,17 @@ run your own data separately if you want):
    Fc = F - ops['neucoeff'] * Fneu
 
    # baseline operation
-   Fc = dcnv.preprocess(Fc, ops)
+   Fc = dcnv.preprocess(
+        F=Fc,
+        baseline=ops['baseline'],
+        win_baseline=ops['win_baseline'],
+        sig_baseline=ops['sig_baseline'],
+        fs=ops['fs'],
+        prctile_baseline=ops['prctile_baseline']
+    )
 
    # get spikes
-   spks = dcnv.oasis(Fc, ops)
+   spks = dcnv.oasis(F=Fc, batch_size=ops['batch_size'], tau=ops['tau'], fs=ops['fs'])
 
 .. _OASIS paper: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005423
 .. _paper: http://www.jneurosci.org/content/38/37/7976

docs/developer_doc.rst

@@ -1,25 +1,42 @@
 Developer Documentation
 ---------------------------
 
+Versioning
+~~~~~~~~~~~~~~~~~~~~~
+There's a rare issue that developers may face when calling `suite2p --version` on their command line. You
+may get an incorrect version number. To fix this issue, one should use the following command:
+
+.. prompt:: bash
+
+        git fetch --prune --unshallow
+
+
 Testing
 ~~~~~~~~~~~~~~~~~~~~~
 
-Before contributing to Suite2P, please make sure your changes pass all our tests. To run the tests (located in
+Before contributing to Suite2P, please make sure your changes pass all our tests.
+
+Downloading Test Data
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To run the tests (located in
 the ``tests`` subdirectory of your working ``suite2p`` directory) , you'll first need to download our test data.
 Suite2p depends on `dvc`_ to download the test data.
 
 .. note::
 
-    Before testing, make sure you have dvc installed:
+    Before testing, make sure you have dvc and pydrive2 installed. Navigate to the suite2p
+    directory and use the following command to install both dvc and pydrive2.
 
     .. prompt:: bash
 
-        pip install dvc
-    The command above may prompt you to install ``pydrive2``. Install it and you should be good to go.
+        pip install -e .[data]
+
+    zsh users should use the following:
 
     .. prompt:: bash
 
-        pip install pydrive2
+        pip install -e .\[docs\]
 
 
 Use to following command to download the test data into the ``data`` subdirectory of your working ``suite2p`` directory.
@@ -28,6 +45,9 @@ Use to following command to download the test data into the ``data`` subdirector
 
     dvc pull
 
+Running the tests
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
 Tests can then be easily run with the following command:
 
 .. prompt:: bash

docs/registration.rst

@@ -209,8 +209,8 @@ To run the script, use the following command:
 
     reg_metrics <INSERT_OPS_DATA_PATH> # Add --tiff_list <INSERT_INPUT_TIF_FILENAME_HERE>.tif to select a subset of tifs
 
-Once you run the ``reg_metrics`` command, registration will be performed for the input file and
-an output similar to the following will be shown:
+Once you run the ``reg_metrics`` command, registration will be performed for the input file with default
+ops parameters and an output similar to the following will be shown:
 
 ::
 
@@ -224,6 +224,14 @@ For each ``nplane``, these statistics (Average and Max) are calculated across PC
 If the registration works perfectly and most of the motion is removed from the registered dataset, these scores
 should all be very close to zero.
 
+.. Important::
+
+    Make sure to also inspect the registered video to check the quality of registration. You can see an example
+    of how this is done in the GUI `here <https://youtu.be/M7UjvCUn74Y?t=810>`_.
+
+You may notice that upon visual inspection, the registered video may look fine/contain little motion even
+if the statistics are not close to zero. You should always visually check the registration output and prioritize
+what your eyes say over what the CLI script reports.
 
 .. note::
 

docs/settings.rst

@@ -65,6 +65,10 @@ Output settings
    to um/pixels in Y (ONLY for correct aspect ratio in GUI, not used for
    other processing)
 
+-  **report_time**: (*bool, default: True) (**new**) whether or not to return
+   a timing dictionary for each plane. Timing dictionary will contain keys
+   corresponding to stages and values corresponding to the duration of that stage.
+
 Registration
 ~~~~~~~~~~~~
 
@@ -121,14 +125,14 @@ Registration
   spatial filtering and tapering (parameters set below), which help
   with 1P registration
 
-- **spatial_hp**: (*int, default: 50*) window in pixels for spatial
+- **spatial_hp**: (*int, default: 42*) window in pixels for spatial
   high-pass filtering before registration
 
-- **pre_smooth**: (*float, default: 2*) if > 0, defines stddev of
+- **pre_smooth**: (*float, default: 0*) if > 0, defines stddev of
   Gaussian smoothing, which is applied before spatial high-pass
   filtering
 
-- **spatial_taper**: (*float, default: 50*) how many pixels to ignore
+- **spatial_taper**: (*float, default: 40*) how many pixels to ignore
   on edges - they are set to zero (important for vignetted windows, for
   FFT padding do not set BELOW 3*ops['smooth_sigma'])
 

environment.yml

@@ -9,6 +9,5 @@ dependencies:
   - matplotlib
   - scipy
   - h5py
-  - scikit-image
   - scikit-learn
   - pyqt