more cleanups

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.

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,

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()