From 127de3605c114487b6dd25cf04a1043f595afd49 Mon Sep 17 00:00:00 2001
From: David Hammer <dhammer@mailbox.org>
Date: Mon, 22 Mar 2021 19:22:19 +0100
Subject: [PATCH] Explicitly set read mode on h5py.File
---
cal_tools/cal_tools/agipdlib.py | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/cal_tools/cal_tools/agipdlib.py b/cal_tools/cal_tools/agipdlib.py
index 019808b84..9fa3e19a0 100644
--- a/cal_tools/cal_tools/agipdlib.py
+++ b/cal_tools/cal_tools/agipdlib.py
@@ -67,7 +67,7 @@ def get_acq_rate(fast_paths: Tuple[str, str, int],
fast_data_file = Path(fast_data_file)
if fast_data_file.is_file():
fast_data_path = f'INSTRUMENT/{karabo_id}/DET/{module}CH0:xtdf/image/pulseId' # noqa
- with h5py.File(fast_data_file) as fin:
+ with h5py.File(fast_data_file, "r") as fin:
if fast_data_path in fin:
# pulses is of shape (NNNN, 1), of type uint8.
# Squeeze out the data, and subtract the 3rd entry from the 2nd
@@ -122,7 +122,7 @@ def get_gain_mode(fname: str, h5path_ctrl: str) -> AgipdGainMode:
h5path_run = h5path_ctrl.replace("CONTROL/", "RUN/", 1)
h5path_gainmode = f'{h5path_run}/gainModeIndex/value'
- with h5py.File(fname, 'r') as fd:
+ with h5py.File(fname, "r") as fd:
if h5path_gainmode in fd:
return AgipdGainMode(fd[h5path_gainmode][0])
return AgipdGainMode.ADAPTIVE_GAIN
@@ -289,20 +289,20 @@ class AgipdCorrections:
data_dict = self.shared_dict[i_proc]
data_dict['moduleIdx'][0] = module_idx
try:
- f = h5py.File(file_name, 'r')
+ f = h5py.File(file_name, "r")
group = f[agipd_base]["image"]
- (_, first_index, last_index,
+ (_, first_index, last_index,
_, valid_indices) = self.get_valid_image_idx(idx_base, f)
allcells = np.squeeze(group['cellId'])
allpulses = np.squeeze(group['pulseId'])
-
+
firange = self.gen_valid_range(first_index, last_index,
self.max_cells, allcells,
allpulses, valid_indices,
apply_sel_pulses)
-
+
n_img = firange.shape[0]
data_dict['nImg'][0] = n_img
if np.all(np.diff(firange) == 1):
@@ -352,7 +352,7 @@ class AgipdCorrections:
return
trains = data_dict['trainId'][:n_img]
- with h5py.File(ofile_name, 'w') as outfile:
+ with h5py.File(ofile_name, "w") as outfile:
# Copy any other data from the input file.
# This includes indexes, so it's important that the corrected data
# we write is aligned with the raw data.
--
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