small fixes from stitching reflectometry files

src/dress/wfm/frames_peakfinding.py

@@ -71,6 +71,8 @@ def frames_peakfinding(data=None,
                        plot=False,
                        verbose=False,
                        nbins=512,
+                       exclude_left=None,
+                       exclude_right=None,
                        bg_threshold=0.05,
                        peak_prominence=0.05,
                        gsmooth=2,
@@ -124,13 +126,13 @@ def frames_peakfinding(data=None,
     bg_value = bg_raw + bg_threshold * (ymax - bg_raw)
     # Find the leading and trailing edges; i.e. the leftmost and rightmost
     # points that exceed the background value
-    i_start = 0
-    i_end = nx - 1
-    for i in range(nx):
+    i_start = exclude_left if exclude_left is not None else 0
+    i_end = exclude_right if exclude_right is not None else nx - 1
+    for i in range(i_start, nx):
         if y[i] > bg_value:
             i_start = i
             break
-    for i in range(nx - 1, 1, -1):
+    for i in range(i_end, 1, -1):
         if y[i] > bg_value:
             i_end = i
             break
@@ -143,9 +145,11 @@ def frames_peakfinding(data=None,
     # Check for unwanted peaks:
     # 1. If a peak is found inside the noise leading the signal, it will often
     # have a zero left base
+    if exclude_left is None:
+        exclude_left = nbins // 10
     to_be_removed = []
     for p in range(len(peaks)):
-        if params["left_bases"][p] < nbins // 10:
+        if params["left_bases"][p] < exclude_left:
             print("Removed peak number {} at x,y = {},{} because of a bad "
                   "left base".format(p, x[peaks[p]], y[peaks[p]]))
             to_be_removed.append(p)
@@ -225,8 +229,8 @@ def frames_peakfinding(data=None,
         fig.savefig(figname, bbox_inches="tight")
 
     frames = {
-        "left_edge": np.array([f[0] for f in frame_boundaries]),
-        "right_edge": np.array([f[1] for f in frame_boundaries]),
+        "left_edges": np.array([f[0] for f in frame_boundaries]),
+        "right_edges": np.array([f[1] for f in frame_boundaries]),
         "gaps": np.array(frame_gaps),
         "shifts": np.array(frame_shifts)
     }

src/dress/wfm/stitch_events.py

@@ -37,7 +37,7 @@ def stitch_events(events=None, frames=None, plot=False, nbins=5000):
     if plot:
         import matplotlib.pyplot as plt
         # Histogram the events for plotting
-        y, edges = np.histogram(time_offset, bins=np.linspace(xmin, xmax, 513))
+        y, edges = np.histogram(time_offset, bins=np.linspace(xmin, xmax, 256))
         x = 0.5 * (edges[:-1] + edges[1:])
         fig, ax = plt.subplots(2, 1, figsize=(8, 8))
         ax[0].plot(x, y, label="Raw data")

src/dress/wfm/stitch_files.py

@@ -71,9 +71,11 @@ def stitch_files(files=None, entries=None, plot=False, frames=None):
         files = files.split(",")
     elif not isinstance(files, list):
         files = [files]
+    print(frames)
 
-    v20setup = v20.setup()
-    v20frames = get_frames(instrument=v20setup)
+    # Compute WFM frame shifts and boundaries from V20 setup
+    if frames is None:
+        frames = get_frames(instrument=v20.setup())
 
     for f in files:
 
@@ -100,11 +102,11 @@ def stitch_files(files=None, entries=None, plot=False, frames=None):
         # Loop through entries and shift event tofs
         with h5py.File(outfile, "r+") as outf:
 
-            # Compute WFM frame shifts and boundaries from V20 setup
-            if frames is None:
-                v20setup = v20.setup(filename=outf)
-                # v20setup = v20.setup()
-                v20frames = get_frames(instrument=v20setup)
+            # # Compute WFM frame shifts and boundaries from V20 setup
+            # if frames is None:
+            #     # v20setup = v20.setup(filename=outf)
+            #     # v20setup = v20.setup()
+            #     # frames = get_frames(instrument=v20.setup(filename=outf))
 
             for e in entries_:
                 print("==================")
@@ -114,11 +116,11 @@ def stitch_files(files=None, entries=None, plot=False, frames=None):
                     this_plot = (outfile + "-" + e + ".pdf").replace("/", "_")
 
                 if e.count("monitor") > 0:
-                    frames = v20frames["monitor"]
+                    frames_ = frames["monitor"]
                 else:
-                    frames = v20frames["DENEX"]
+                    frames_ = frames["DENEX"]
 
                 _stitch_file(file_handle=outf,
                              entry=e,
-                             frames=frames,
+                             frames=frames_,
                              plot=this_plot)