diff --git a/Jenkinsfile b/Jenkinsfile index b7e0ca0ae..92e5c8506 100644 --- a/Jenkinsfile +++ b/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: diff --git a/bin/caiman_gui.py b/bin/caiman_gui.py index 6d1fd68f8..abc1121af 100755 --- a/bin/caiman_gui.py +++ b/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 diff --git a/caiman/behavior/behavior.py b/caiman/behavior/behavior.py index 9d9b1abcd..2f0a49dc0 100644 --- a/caiman/behavior/behavior.py +++ b/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 diff --git a/caiman/mmapping.py b/caiman/mmapping.py index 0f3571242..532ae296c 100644 --- a/caiman/mmapping.py +++ b/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 diff --git a/caiman/source_extraction/cnmf/cnmf.py b/caiman/source_extraction/cnmf/cnmf.py index 520f6e70a..0233dd349 100644 --- a/caiman/source_extraction/cnmf/cnmf.py +++ b/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 diff --git a/caiman/source_extraction/cnmf/deconvolution.py b/caiman/source_extraction/cnmf/deconvolution.py index 23ed567c8..6d185c63a 100644 --- a/caiman/source_extraction/cnmf/deconvolution.py +++ b/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 diff --git a/caiman/source_extraction/cnmf/map_reduce.py b/caiman/source_extraction/cnmf/map_reduce.py index 723175d5e..5a629a028 100644 --- a/caiman/source_extraction/cnmf/map_reduce.py +++ b/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 diff --git a/caiman/source_extraction/volpy/mrcnn/model.py b/caiman/source_extraction/volpy/mrcnn/model.py index d4bd4c3b1..2dee5f23f 100644 --- a/caiman/source_extraction/volpy/mrcnn/model.py +++ b/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))] diff --git a/caiman/source_extraction/volpy/mrcnn/neurons.py b/caiman/source_extraction/volpy/mrcnn/neurons.py index 61fcc871a..6e59c2c3b 100644 --- a/caiman/source_extraction/volpy/mrcnn/neurons.py +++ b/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] diff --git a/caiman/source_extraction/volpy/spikepursuit.py b/caiman/source_extraction/volpy/spikepursuit.py index b5f45e36d..c42bc3a47 100644 --- a/caiman/source_extraction/volpy/spikepursuit.py +++ b/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: diff --git a/caiman/source_extraction/volpy/volpy.py b/caiman/source_extraction/volpy/volpy.py index c81cec027..0039f5612 100644 --- a/caiman/source_extraction/volpy/volpy.py +++ b/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 diff --git a/caiman/tests/comparison/comparison.py b/caiman/tests/comparison/comparison.py index 7c6ae24c4..24f176a99 100644 --- a/caiman/tests/comparison/comparison.py +++ b/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) diff --git a/caiman/tests/comparison_humans.py b/caiman/tests/comparison_humans.py index b8a29c0e6..4ab28b3c0 100644 --- a/caiman/tests/comparison_humans.py +++ b/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)