Merge pull request #198 from scottclowe/api_deltaf-raw-shape

API: Change the shape of deltaf_raw to have the same number of dimensions as other outputs
rochefort-lab · Jun 29, 2021 · 8296a6c · 8296a6c
2 parents f061d4e + a4633f2
commit 8296a6c
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Showing 5 changed files with 9 additions and 9 deletions.
diff --git a/examples/Basic usage.ipynb b/examples/Basic usage.ipynb
@@ -279,7 +279,7 @@
     "t = 1\n",
     "\n",
     "(\n",
-    "    hv.Curve(experiment.deltaf_raw[c][t], label=\"Raw\", vdims=[\"df/f0\"])\n",
+    "    hv.Curve(experiment.deltaf_raw[c][t][0, :], label=\"Raw\", vdims=[\"df/f0\"])\n",
     "    * hv.Curve(experiment.deltaf_result[c, t][0, :], label=\"Decontaminated\")\n",
     ")"
    ]

diff --git a/fissa/core.py b/fissa/core.py
@@ -395,14 +395,18 @@ class Experiment:
 
     deltaf_raw : :class:`numpy.ndarray`
         A :class:`numpy.ndarray` of shape ``(n_rois, n_trials)``, each element
-        of which is itself a :class:`numpy.ndarray` shaped ``(n_timepoint, )``.
+        of which is itself a :class:`numpy.ndarray` shaped ``(1, n_timepoint)``.
 
         The amount of change in fluorence relative to the baseline fluorence
         (Δf/f\ :sub:`0`).
 
         This field is only populated after :meth:`calc_deltaf` has been run;
         until then, it is set to ``None``.
 
+        .. versionchanged:: 1.0.0
+            The shape of the interior arrays changed from ``(n_timepoint, )``
+            to ``(1, n_timepoint)``.
+
     deltaf_result : :class:`numpy.ndarray`
         A :class:`numpy.ndarray` of shape ``(n_rois, n_trials)``, each element
         of which is itself a :class:`numpy.ndarray` shaped
@@ -964,7 +968,7 @@ def calc_deltaf(self, freq, use_raw_f0=True, across_trials=True):
                 for trial in range(self.nTrials):
                     nextTrial = curTrial + self.raw[cell][trial].shape[1]
                     signal = raw_conc[curTrial:nextTrial]
-                    deltaf_raw[cell][trial] = signal
+                    deltaf_raw[cell][trial] = np.expand_dims(signal, axis=0)
                     signal = result_conc[:, curTrial:nextTrial]
                     deltaf_result[cell][trial] = signal
                     curTrial = nextTrial
@@ -986,7 +990,7 @@ def calc_deltaf(self, freq, use_raw_f0=True, across_trials=True):
                         result_sig = (result_sig - result_f0) / result_f0
 
                     # store deltaf/f0s
-                    deltaf_raw[cell][trial] = raw_sig
+                    deltaf_raw[cell][trial] = np.expand_dims(raw_sig, axis=0)
                     deltaf_result[cell][trial] = result_sig
 
         self.deltaf_raw = deltaf_raw

diff --git a/fissa/tests/resources/b/expected_py2.npz b/fissa/tests/resources/b/expected_py2.npz
diff --git a/fissa/tests/resources/b/expected_py3.npz b/fissa/tests/resources/b/expected_py3.npz
diff --git a/fissa/tests/test_core.py b/fissa/tests/test_core.py
@@ -178,12 +178,8 @@ def compare_matlab(self, fname, experiment, compare_deltaf=None):
                 M["df_result"][0, 0][0][0, 0][0],
                 experiment.deltaf_result[0, 0],
             )
-            # Row and column vectors on MATLAB are 2d instead of 1d, and df_raw
-            # is a vector, not a matrix, so has an extra dimension.
-            # N.B. This extra dimension is in the wrong place as it doesn't align
-            # with the other attributes.
             self.assert_allclose(
-                M["df_raw"][0, 0][0][0, 0][0][0, :],
+                M["df_raw"][0, 0][0][0, 0][0],
                 experiment.deltaf_raw[0, 0],
             )