diff --git a/src/cristallina/analysis.py b/src/cristallina/analysis.py index ea7344f..a6f05aa 100644 --- a/src/cristallina/analysis.py +++ b/src/cristallina/analysis.py @@ -178,29 +178,6 @@ def sum_images( ) -def get_contrast_images( - filesets, - channel="JF16T03V01", - alignment_channels=None, - batch_size=10, - roi: Optional[ROI] = None, - preview=False, -): - """ - See perform_image_calculations. Here calculates mean and standard deviation for a given set of images. - """ - - return perform_image_calculations( - filesets, - channel=channel, - alignment_channels=alignment_channels, - batch_size=batch_size, - roi=roi, - preview=preview, - operations=["mean", "std"], - ) - - @memory.cache(ignore=["batch_size"]) # we ignore batch_size for caching purposes def perform_image_stack_sum( filesets, @@ -213,7 +190,7 @@ def perform_image_stack_sum( upper_cutoff_threshold=None, # in keV ): """ - Performs summation for a given region of interest (roi) for an image channel + Performs summation along the pulse dimensionfor a given region of interest (roi) for an image channel from a fileset (e.g. "run0352/data/acq0001.*.h5" or step.fnames from a SFScanInfo object). Allows alignment, i.e. reducing only to a common subset with other channels. diff --git a/src/cristallina/plot.py b/src/cristallina/plot.py index e691724..ce36ff6 100644 --- a/src/cristallina/plot.py +++ b/src/cristallina/plot.py @@ -1,4 +1,3 @@ -import re from collections import defaultdict import matplotlib @@ -27,7 +26,7 @@ plt.style.use("cristallina.cristallina_style") def ju_patch_less_verbose(ju_module): """Quick monkey patch to suppress verbose messages from gain & pedestal file searcher. - Not required for newer versions of ju.""" + Not anymore required for newer versions of ju.""" if hasattr(ju_module, "swissfel_helpers"): @@ -273,6 +272,7 @@ def plot_spectrum_channel(data: SFDataFiles, channel_name_x, channel_name_y, ave ax.set_xlabel(channel_name_x) axis_styling(ax, channel_name_y, description) + def line_plot_with_colorbar(xs,ys,colors, cmap=plt.cm.viridis, markers='o',markersize=6,alpha=1, title=None,xlabel=None,ylabel=None,cbar_label=None, diff --git a/src/cristallina/utils.py b/src/cristallina/utils.py index 4616624..e835814 100644 --- a/src/cristallina/utils.py +++ b/src/cristallina/utils.py @@ -333,7 +333,7 @@ def check_JF_frames(JF_file_path): Raises an error if invalid frames are found, else returns True. """ pattern = r"\.(JF[0-9].*)\.h5" - m = re.search(pattern, str(fpath)) + m = re.search(pattern, str(JF_file_path)) if m is None: raise LookupError("Cannot match Jungfrau detector name from file path.") @@ -346,6 +346,7 @@ def check_JF_frames(JF_file_path): else: return True + def get_step_time(step: SFDataFiles): """Returns the start and end time as a unix timestamp (in seconds) of a given SFDataFiles or scan step. @@ -360,9 +361,6 @@ def get_step_time(step: SFDataFiles): ) / np.timedelta64(1, "s") - - - def wait_for_run(run_number, total_num_steps, snd_file_path="/tmp/CantinaBand3.wav"): """ Busy wait loop until run has completed all steps. Plays sound when all files are written to disk. @@ -637,7 +635,7 @@ def find_nearest(array, value): def find_two_nearest(time_array, percentage): - """Finds indeces of the two values that are the nearest to the given value in an array""" + """Finds indices of the two values that are the nearest to the given value in an array""" array = np.asarray(time_array) value = (np.max(array) - np.min(array)) * percentage + np.min(array) idx = (np.abs(array - value)).argmin()