Add allen institute vendored code + Neuropil subtraction exploration

derotation/postprocessing/neuropil_subtraction.py

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+import vendor.allensdk.brain_observatory.dff as dff_module
+from vendor.allensdk.brain_observatory.r_neuropil import NeuropilSubtract
+
+
+def neuropil_subtraction(f, f_neu) -> tuple:
+    """Compute neuropil subtraction and dF/F for a given ROI
+
+    Parameters
+    ----------
+    f : np.ndarray
+        Fluorescence trace of the ROI
+    f_neu : np.ndarray
+        Fluorescence trace of the neuropil
+
+    Returns
+    -------
+    tuple(np.ndarray, np.ndarray)
+        dF/F and neuropil signal
+    """
+    neuropil_subtraction = NeuropilSubtract()
+    neuropil_subtraction.set_F(f, f_neu)
+    neuropil_subtraction.fit()
+
+    r = neuropil_subtraction.r
+
+    f_corr = f - r * f_neu
+
+    # kernel values to be chossen for 3-photon data
+    dff = 100 * dff_module.compute_dff_windowed_median(
+        f_corr, median_kernel_long=1213, median_kernel_short=23
+    )
+
+    return dff, r

vendor/allensdk/LICENSE

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+Allen Institute Software License - This software license is the 2-clause BSD
+license plus a third clause that prohibits redistribution for commercial
+purposes without further permission.
+
+Copyright 2017. Allen Institute. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+3. Redistributions for commercial purposes are not permitted without the
+Allen Institute's written permission.
+For purposes of this license, commercial purposes is the incorporation of the
+Allen Institute's software into anything for which you will charge fees or
+other compensation. Contact [email protected] for commercial licensing
+opportunities.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.