diff --git a/cal_tools/cal_tools/agipdlib.py b/cal_tools/cal_tools/agipdlib.py
index b7a482f51bb7edf4dc0f0e23779db1fb9df8d7a5..a363531f5b73e2902d4838d41714673bdc842c3d 100644
--- a/cal_tools/cal_tools/agipdlib.py
+++ b/cal_tools/cal_tools/agipdlib.py
@@ -121,7 +121,10 @@ class AgipdCorrections:
self.index_v = raw_fmt_version
self.chunksize = chunk_size
self.initialized = False
- self.pulses_lst = list(range(*max_pulses))
+ self.rng_pulses = max_pulses
+ # avoid list(range(*[0]]))
+ self.pulses_lst = list(range(*max_pulses)) \
+ if not (len(max_pulses) == 1 and max_pulses[0] == 0) else max_pulses #noqa
self.min_pulse = self.pulses_lst[0]
self.max_pulse = self.pulses_lst[-1]
self.max_cells = max_cells
@@ -1035,17 +1038,24 @@ class AgipdCorrections:
if cidx == 0:
copim = copy.copy(im)
copim[copim < self.median_noise] = np.nan
- bins = (self.bins_signal_low_range, self.max_pulse)
+
+ # avoid 0 hist_pulses, otherwise histogram plot will fail
+ if self.max_pulse == 0:
+ self.hist_pulses = int(self.max_pulse + 1)
+ else:
+ self.hist_pulses = self.max_pulse
+
+ bins = (self.bins_signal_low_range, self.hist_pulses)
rnge = [[-50, 1000], [self.min_pulse,
self.max_pulse + 1]]
H, xe, ye = np.histogram2d(np.nanmean(copim, axis=(1, 2)),
pulseId,
bins=bins,
range=rnge)
- self.hist_pulses = self.max_pulse
+
self.hists_signal_low += H
self.low_edges = (xe, ye)
- bins = (self.bins_signal_high_range, self.max_pulse)
+ bins = (self.bins_signal_high_range, self.hist_pulses)
rnge = [[0, 200000], [self.min_pulse,
self.max_pulse + 1]]
H, xe, ye = np.histogram2d(np.nanmean(copim, axis=(1, 2)),
@@ -1165,11 +1175,12 @@ class AgipdCorrections:
single_image = np.array(single_image)
# Calculate the pulse step from the chosen max_pulse range
- # This is not calculated from max_pulses[2],
- # as it might not be available.
- pulse_step = self.pulses_lst[1] - self.pulses_lst[0]
+ if len(self.rng_pulses) == 3:
+ pulse_step = self.rng_pulses[2]
+ else:
+ pulse_step = 1
- # Make sure the range max doesn't have non valid idx.
+ # Make sure the range max doesn't have non-valid idx.
if self.pulses_lst[-1] + pulse_step > last_index-1:
last_pulse = last_index-1
else:
@@ -1177,7 +1188,7 @@ class AgipdCorrections:
# Check if 1st pulse idx was out of valid range.
# If that is the case only calibrate the last step pulse.
if self.pulses_lst[0] >= last_pulse:
- first_pulse = self.pulses_lst[0] - pulse_step
+ first_pulse = last_pulse - pulse_step
else:
first_pulse = self.pulses_lst[0]
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index 8ca55e0c4eceb19199f13bed76a0090900d5d0e9..d7b7f9be6c199c4ef470ad393796d70bce679a58 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -22,8 +22,8 @@
},
"outputs": [],
"source": [
- "in_folder = \"/gpfs/exfel/exp/MID/201931/p900090/raw\" # the folder to read data from, required\n",
- "run = 563 # runs to process, required\n",
+ "in_folder = \"/gpfs/exfel/exp/MID/201931/p900107/raw\" # the folder to read data from, required\n",
+ "run = 11 # runs to process, required\n",
"out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/AGIPD_Corr\" # the folder to output to, required\n",
"calfile = \"/gpfs/exfel/data/scratch/haufs/agipd_on_demand/agipd_store_mid.h5\" # path to calibration file. Leave empty if all data should come from DB\n",
"sequences = [-1] # sequences to correct, set to -1 for all, range allowed\n",
@@ -503,11 +503,18 @@
"inp = []\n",
"left = total_sequences\n",
"\n",
- "pulses_lst = list(range(*max_pulses))\n",
- "print(\"A range of {} pulse indices is selected: from {} to {} with a step of {}\"\n",
+ "pulses_lst = list(range(*max_pulses)) if not (len(max_pulses)==1 and max_pulses[0]==0) else max_pulses \n",
+ "\n",
+ "try:\n",
+ " if len(pulses_lst) > 1: \n",
+ " print(\"A range of {} pulse indices is selected: from {} to {} with a step of {}\"\n",
" .format(len(pulses_lst), pulses_lst[0] , pulses_lst[-1] + (pulses_lst[1] - pulses_lst[0]),\n",
" pulses_lst[1] - pulses_lst[0]))\n",
- "\n",
+ " else:\n",
+ " print(\"one pulse is selected: a pulse of idx {}\".format(pulses_lst[0]))\n",
+ "except Exception as e:\n",
+ " raise ValueError('max_pulses input Error: {}'.format(e))\n",
+ " \n",
"bins_gain_vs_signal = (100, 100)\n",
"bins_signal_low_range = 100\n",
"bins_signal_high_range = 100\n",
@@ -1139,6 +1146,13 @@
"cb = fig.colorbar(im, ax=ax)"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
{
"cell_type": "code",
"execution_count": null,
diff --git a/webservice/update_config.py b/webservice/update_config.py
index e70548aa44728c81ec63d9b1cf1b77a1464a4acc..d1972e6e6091b9a8b050b7817b5a8171f31e17e6 100644
--- a/webservice/update_config.py
+++ b/webservice/update_config.py
@@ -80,9 +80,13 @@ for key, value in args.items():
if 'no-' in key and isinstance(value, bool):
if key not in bool_keys:
- new_conf[task][instrument][detector][key.replace('no-','')] = False
+ new_conf[task][instrument][detector][key.replace('no-','')] = False #noqa
# avoid saving the "no-"key into the updated config
continue
+ # Assure adding an empty string for new empty
+ # str. updates (e.g. calfile)
+ if isinstance(key, str) and (value == '' or value == ' '):
+ value = '""'
new_conf[task][instrument][detector][key] = value