Merge pull request #547 from MouseLand/dev

Dev

Author: carsen-stringer

.travis.yml

@@ -57,7 +57,7 @@ install:
 - dvc pull -r gdrive-travis
 - pip install coveralls
 script:
-- coverage run --source=suite2p setup.py test
+- coverage run --source=suite2p --omit=suite2p/gui/* setup.py test
 after_success: coveralls
 deploy:
   skip_cleanup: true

setup.py

@@ -29,6 +29,20 @@
         'sphinx_rtd_theme',
         'sphinx-prompt',
         'sphinx-autodoc-typehints',
+        'importlib-metadata',
+        'natsort',
+        'rastermap>0.1.0',
+        'tifffile',
+        'scanimage-tiff-reader>=1.4.1',
+        'pyqtgraph',
+        'importlib-metadata',
+        'paramiko',
+        'numpy>=1.16',
+        'numba>=0.43.1',
+        'matplotlib',
+        'scipy',
+        'h5py',
+        'scikit-learn',
       ],
       # Note: Available in pypi, but cleaner to install as pyqt from conda.
       "gui": [

suite2p/registration/bidiphase.py

@@ -2,15 +2,13 @@
 from numpy import fft
 
 
-def compute(frames) -> int:
-    """ computes the bidirectional phase offset
-
-    sometimes in line scanning there will be offsets between lines;
-    if ops['do_bidiphase'], then bidiphase is computed and applied
+def compute(frames: np.ndarray) -> int:
+    """
+    Returns the bidirectional phase offset, the offset between lines that sometimes occurs in line scanning.
 
     Parameters
     ----------
-    frames : int16
+    frames : frames x Ly x Lx
         random subsample of frames in binary (frames x Ly x Lx)
 
     Returns
@@ -38,14 +36,12 @@ def compute(frames) -> int:
 
 
 def shift(frames: np.ndarray, bidiphase: int) -> None:
-    """ shift frames by bidirectional phase offset in-place, bidiphase
-
-    sometimes in line scanning there will be offsets between lines;
-    shifts last axis by bidiphase
+    """
+    Shift last axis of 'frames' by bidirectional phase offset in-place, bidiphase.
 
     Parameters
     ----------
-    frames : (frames x Ly x Lx)
+    frames : frames x Ly x Lx
     bidiphase : int
         bidirectional phase offset in pixels
     """

suite2p/registration/metrics.py

@@ -16,30 +16,32 @@
 from .. import io
 
 def pclowhigh(mov, nlowhigh, nPC, random_state):
-    """ get mean of top and bottom PC weights for nPC's of mov
-
-        computes nPC PCs of mov and returns average of top and bottom
-
-        Parameters
-        ----------
-        mov : int16, array
-            subsampled frames from movie size frames x Ly x Lx
-        nlowhigh : int
-            number of frames to average at top and bottom of each PC
-        nPC : int
-            number of PCs to compute
-
-        Returns
-        -------
-            pclow : float, array
-                average of bottom of spatial PC: nPC x Ly x Lx
-            pchigh : float, array
-                average of top of spatial PC: nPC x Ly x Lx
-            w : float, array
-                singular values of decomposition of mov
-            v : float, array
-                frames x nPC, how the PCs vary across frames
-
+    """
+    Compute mean of top and bottom PC weights for nPC's of mov
+
+    computes nPC PCs of mov and returns average of top and bottom
+
+    Parameters
+    ----------
+    mov : frames x Ly x Lx
+        subsampled frames from movie
+    nlowhigh : int
+        number of frames to average at top and bottom of each PC
+    nPC : int
+        number of PCs to compute
+    random_state:
+        a value that sets the seed for the PCA randomizer.
+
+    Returns
+    -------
+        pclow : float, array
+            average of bottom of spatial PC: nPC x Ly x Lx
+        pchigh : float, array
+            average of top of spatial PC: nPC x Ly x Lx
+        w : float, array
+            singular values of decomposition of mov
+        v : float, array
+            frames x nPC, how the PCs vary across frames
     """
     nframes, Ly, Lx = mov.shape
     mov = mov.reshape((nframes, -1))
@@ -63,31 +65,44 @@ def pclowhigh(mov, nlowhigh, nPC, random_state):
 def pc_register(pclow, pchigh, bidi_corrected, spatial_hp=None, pre_smooth=None, smooth_sigma=1.15, smooth_sigma_time=0,
                 block_size=(128,128), maxregshift=0.1, maxregshiftNR=10, reg_1p=False, snr_thresh=1.25,
                 is_nonrigid=True, pad_fft=False, bidiphase=0, spatial_taper=50.0):
-    """ register top and bottom of PCs to each other
-
-        Parameters
-        ----------
-        pclow : float, array
-            average of bottom of spatial PC: nPC x Ly x Lx
-        pchigh : float, array
-            average of top of spatial PC: nPC x Ly x Lx
-        refImg : int16, array
-            reference image from registration
-        smooth_sigma : :obj:`int`, optional
-            default 1.15, see registration settings
-        block_size : :obj:`tuple`, optional
-            default (128,128), see registration settings
-        maxregshift : :obj:`float`, optional
-            default 0.1, see registration settings
-        maxregshiftNR : :obj:`int`, optional
-            default 10, see registration settings
-        1Preg : :obj:`bool`, optional
-            default True, see 1Preg settings
-
-        Returns
-        -------
-            X : float, array
-                nPC x 3 where X[:,0] is rigid, X[:,1] is average nonrigid, X[:,2] is max nonrigid shifts
+    """
+    register top and bottom of PCs to each other
+
+    Parameters
+    ----------
+    pclow : float, array
+        average of bottom of spatial PC: nPC x Ly x Lx
+    pchigh : float, array
+        average of top of spatial PC: nPC x Ly x Lx
+    bidi_corrected: bool
+        whether to do bidi correction.
+    spatial_hp: int
+        high-pass filter window size for the spatial dimensions
+    pre_smooth: int
+        low-pass filter window size for the spatial dimensions
+    smooth_sigma : int
+        see registration settings
+    smooth_sigma_time: int
+        see registration settings
+    block_size : int, int
+        see registration settings
+    maxregshift : float
+        see registration settings
+    maxregshiftNR : int
+        see registration settings
+    reg_1p : bool
+        see 1Preg settings
+    snr_thresh: float
+        signal to noise threshold to use.
+    is_nonrigid: bool
+    pad_fft: bool
+    bidiphase: int
+    spatial_taper: float
+
+    Returns
+    -------
+        X : float array
+            nPC x 3 where X[:,0] is rigid, X[:,1] is average nonrigid, X[:,2] is max nonrigid shifts
     """
     # registration settings
     nPC, Ly, Lx = pclow.shape
@@ -176,28 +191,27 @@ def pc_register(pclow, pchigh, bidi_corrected, spatial_hp=None, pre_smooth=None,
 
 
 def get_pc_metrics(ops, use_red=False):
-    """ computes registration metrics using top PCs of registered movie
-
-        movie saved as binary file ops['reg_file']
-        metrics saved to ops['regPC'] and ops['X']
-        'regDX' is nPC x 3 where X[:,0] is rigid, X[:,1] is average nonrigid, X[:,2] is max nonrigid shifts
-        'regPC' is average of top and bottom frames for each PC
-        'tPC' is PC across time frames
-
-        Parameters
-        ----------
-        ops : dictionary
-            'nframes', 'Ly', 'Lx', 'reg_file' (if use_red=True, 'reg_file_chan2')
-            (optional, 'refImg', 'block_size', 'maxregshiftNR', 'smooth_sigma', 'maxregshift', '1Preg')
-        use_red : :obj:`bool`, optional
-            default False, whether to use 'reg_file' or 'reg_file_chan2'
-        nPC : int
-            # n PCs to compute motion for
-
-        Returns
-        -------
-            ops : dictionary
-                adds 'regPC' and 'tPC' and 'regDX'
+    """
+    Computes registration metrics using top PCs of registered movie
+
+    movie saved as binary file ops['reg_file']
+    metrics saved to ops['regPC'] and ops['X']
+    'regDX' is nPC x 3 where X[:,0] is rigid, X[:,1] is average nonrigid, X[:,2] is max nonrigid shifts
+    'regPC' is average of top and bottom frames for each PC
+    'tPC' is PC across time frames
+
+    Parameters
+    ----------
+    ops : dict
+        'nframes', 'Ly', 'Lx', 'reg_file' (if use_red=True, 'reg_file_chan2')
+        (optional, 'refImg', 'block_size', 'maxregshiftNR', 'smooth_sigma', 'maxregshift', '1Preg')
+    use_red : :obj:`bool`, optional
+        default False, whether to use 'reg_file' or 'reg_file_chan2'
+
+    Returns
+    -------
+    ops : dict
+        The same as the ops input, but will now include 'regPC', 'tPC', and 'regDX'.
 
     """
     random_state = ops['reg_metrics_rs'] if 'reg_metrics_rs' in ops else None