[DATALAD RUNCMD] Do interactive fixing of some ambigous typos

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w -i 3 -C 2",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

Jenkinsfile

@@ -94,7 +94,7 @@ Check console output at $BUILD_URL to view full results.
 Building $BRANCH_NAME for $CAUSE
 $JOB_DESCRIPTION
 
-Chages:
+Changes:
 $CHANGES
 
 End of build log:

bin/caiman_gui.py

@@ -113,7 +113,7 @@ def selectionchange(self,i):
 def rotate90(img, right=None, vector=None, sparse=False):
     # rotate the img 90 degrees
     # we first transpose the img then flip axis
-    # If right is ture, then rotate 90 degrees right, otherwise, rotate left
+    # If right is true, then rotate 90 degrees right, otherwise, rotate left
     # If vector is True, then we first reshape the spatial 1D vector to 2D then rotate
     # If vector is False, then we directly rotate the matrix
     global dims

caiman/behavior/behavior.py

@@ -178,7 +178,7 @@ def compute_optical_flow(m,
             mask selecting relevant pixels
 
         polar_coord: boolean
-            wheather to return the coordinate in polar coordinates (or cartesian)
+            whether to return the coordinate in polar coordinates (or cartesian)
 
         do_show: bool
             show flow movie

caiman/mmapping.py

@@ -90,7 +90,7 @@ def save_memmap_each(fnames: list[str],
             list of path to the filenames
 
         dview: ipyparallel dview
-            used to perform computation in parallel. If none it will be signle thread
+            used to perform computation in parallel. If none it will be single thread
 
         base_name str
             BaseName for the file to be creates. If not given the file itself is used

caiman/source_extraction/cnmf/cnmf.py

@@ -392,7 +392,7 @@ def fit_file(self, motion_correct=False, indices=None, include_eval=False):
 
     def refit(self, images, dview=None):
         """
-        Refits the data using CNMF initialized from a previous interation
+        Refits the data using CNMF initialized from a previous iteration
 
         Args:
             images

caiman/source_extraction/cnmf/deconvolution.py

@@ -552,7 +552,7 @@ def onnls(y, g, lam=0, shift=100, window=None, mask=None, tol=1e-9, max_iter=Non
         shift : int, optional, default 100
             Number of frames by which to shift window from on run of NNLS to the next.
     
-        window : int, optional, default None (200 or larger dependend on g)
+        window : int, optional, default None (200 or larger dependent on g)
             Window size.
     
         mask : array of bool, shape (n,), optional, default (True,)*n
@@ -671,7 +671,7 @@ def constrained_oasisAR2(y, g, sn, optimize_b=True, b_nonneg=True, optimize_g=0,
         shift : int, optional, default 100
             Number of frames by which to shift window from on run of NNLS to the next.
     
-        window : int, optional, default None (200 or larger dependend on g)
+        window : int, optional, default None (200 or larger dependent on g)
             Window size.
     
         tol : float, optional, default 1e-9

caiman/source_extraction/cnmf/map_reduce.py

@@ -25,7 +25,7 @@ def cnmf_patches(args_in):
             file_name: string
                 full path to an npy file (2D, pixels x time) containing the movie
 
-            shape: tuple of thre elements
+            shape: tuple of three elements
                 dimensions of the original movie across y, x, and time
 
             params:
@@ -48,7 +48,7 @@ def cnmf_patches(args_in):
 
             memory_fact: double
                 unitless number accounting how much memory should be used.
-                It represents the fration of patch processed in a single thread.
+                It represents the fraction of patch processed in a single thread.
                  You will need to try different values to see which one would work
 
             low_rank_background: bool
@@ -150,7 +150,7 @@ def run_CNMF_patches(file_name, shape, params, gnb=1, dview=None,
 
         memory_fact: double
             unitless number accounting how much memory should be used.
-            It represents the fration of patch processed in a single thread.
+            It represents the fraction of patch processed in a single thread.
              You will need to try different values to see which one would work
 
         border_pix: int

caiman/source_extraction/volpy/mrcnn/model.py

@@ -1091,7 +1091,7 @@ def rpn_bbox_loss_graph(config, target_bbox, rpn_match, rpn_bbox):
 
     config: the model config object.
     target_bbox: [batch, max positive anchors, (dy, dx, log(dh), log(dw))].
-        Uses 0 padding to fill in unsed bbox deltas.
+        Uses 0 padding to fill in unused bbox deltas.
     rpn_match: [batch, anchors, 1]. Anchor match type. 1=positive,
                -1=negative, 0=neutral anchor.
     rpn_bbox: [batch, anchors, (dy, dx, log(dh), log(dw))]

caiman/source_extraction/volpy/mrcnn/neurons.py

@@ -158,7 +158,7 @@ def load_neurons(self, dataset_dir, subset):
             
             # load_mask() needs the image size to convert polygons to masks.
             # Unfortunately, VIA doesn't include it in JSON, so we must read
-            # the image. This is only managable since the dataset is tiny.
+            # the image. This is only manageable since the dataset is tiny.
             image_path = os.path.join(dataset_dir, a)
             image = np.load(image_path)['arr_0']
             height, width = image.shape[:2]

caiman/source_extraction/volpy/spikepursuit.py

@@ -104,7 +104,7 @@ def volspike(pars):
                         ridge or NMF for weight update
                         
                     do_plot: boolean
-                        if Ture, plot trace of signals and spiketimes, 
+                        if True, plot trace of signals and spiketimes, 
                         peak triggered average, histogram of heights in the last iteration
 
                     do_cross_val: boolean
@@ -431,7 +431,7 @@ def denoise_spikes(data, window_length, fr=400,  hp_freq=1,  clip=100, threshold
             The real threshold is the value multiply estimated noise level
 
         do_plot: boolean
-            if Ture, will plot trace of signals and spiketimes, peak triggered
+            if True, will plot trace of signals and spiketimes, peak triggered
             average, histogram of heights
             
     Returns:

caiman/source_extraction/volpy/volpy.py

@@ -93,7 +93,7 @@ def __init__(self, n_processes, dview=None, template_size=0.02, context_size=35,
                 ridge or NMF for weight update
                 
             do_plot: boolean
-                if Ture, plot trace of signals and spiketimes, 
+                if True, plot trace of signals and spiketimes, 
                 peak triggered average, histogram of heights in the last iteration
 
             do_cross_val: boolean

caiman/tests/comparison/comparison.py

@@ -143,7 +143,7 @@ def save_with_compare(self, istruth=False, params=None, dview=None, Cn=None):
         """save the comparison as well as the images of the precision recall calculations
 
 
-            depending on if we say this file will be ground truth or not, it wil be saved in either the tests or the ground truth folder
+            depending on if we say this file will be ground truth or not, it will be saved in either the tests or the ground truth folder
             if saved in test, a comparison to groundtruth will be added to the object 
             this comparison will be on 
                 data : a normized difference of the normalized value of the arrays
@@ -156,10 +156,10 @@ def save_with_compare(self, istruth=False, params=None, dview=None, Cn=None):
 
             Args:
                 self:  dictionary
-                   the object of this class tha tcontains every value
+                   the object of this class that tcontains every value
 
                 istruth: Boolean
-                    if we want it ot be the ground truth
+                    if we want it to be the ground truth
 
                 params:
                     movie parameters
@@ -250,7 +250,7 @@ def save_with_compare(self, istruth=False, params=None, dview=None, Cn=None):
                     C_full = dt['C_full'][()]
                     C_patch = dt['C_patch'][()]
                     data = dt['information'][()]
-                                                                                                            # if we cannot manage to open it or it doesnt exist:
+                                                                                                            # if we cannot manage to open it or it doesn't exist:
             except (IOError, OSError):
                                                                                                             # we save but we explain why there were a problem
                 logging.warning('we were not able to read the file ' + str(file_path) + ' to compare it\n')
@@ -364,7 +364,7 @@ def see(filename=None):
 
         Args:
             self:  dictionary
-                the object of this class tha tcontains every value
+                the object of this class that tcontains every value
             filename:
                 ( just give the number or name)
 

caiman/tests/comparison_humans.py

@@ -422,7 +422,7 @@
                                       thresh_subset=0.6)
     gt_estimate.select_components(use_object=True)
     print(gt_estimate.A_thr.shape)
-    # %% prepare CNMF maks
+    # %% prepare CNMF mask
     cnm2.estimates.threshold_spatial_components(maxthr=0.2, dview=dview)
     cnm2.estimates.remove_small_large_neurons(min_size_neuro, max_size_neuro)
     cnm2.estimates.remove_duplicates(r_values=None, dist_thr=0.1, min_dist=10, thresh_subset=0.6)