From 52eaa01cc4e03be3c2abda306531d55a2807528f Mon Sep 17 00:00:00 2001
From: Cyril Danilevski <cydanil@gmail.com>
Date: Thu, 12 Aug 2021 21:37:52 +0200
Subject: [PATCH] Remove driver=core from AGIPD notebooks
---
notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb | 2 +-
notebooks/AGIPD/playground/AGIPD-Gain_Distributions.ipynb | 2 +-
notebooks/AGIPD/playground/AGIPD_SingleM_test_Dark.ipynb | 2 +-
notebooks/AGIPD/playground/Characterize_AGIPD_CI.ipynb | 2 +-
.../AGIPD/playground/Characterize_AGIPD_Dark-batch.ipynb | 4 ++--
.../playground/Characterize_AGIPD_Gain_CompareXGM.ipynb | 2 +-
.../AGIPD/playground/Characterize_AGIPD_Gain_Darks.ipynb | 2 +-
.../playground/Characterize_AGIPD_Gain_FlatFields.ipynb | 6 +++---
.../Characterize_AGIPD_Gain_FlatFields_Coupling.ipynb | 2 +-
.../playground/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb | 6 +++---
.../playground/Characterize_AGIPD_Gain_Transition.ipynb | 4 ++--
.../AGIPD/playground/Characterize_AGIPD_Pulse_Cell.ipynb | 6 +++---
notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC.ipynb | 4 ++--
.../AGIPD/playground/Chracterize_AGIPD_Gain_PC_KMeans.ipynb | 2 +-
.../AGIPD/playground/Chracterize_AGIPD_Gain_PC_mlearn.ipynb | 4 ++--
notebooks/AGIPD/playground/Correct_AGIPD-Verify.ipynb | 4 ++--
notebooks/AGIPD/playground/Correct_AGIPD-batch.ipynb | 4 ++--
17 files changed, 29 insertions(+), 29 deletions(-)
diff --git a/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb b/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
index c6dc6f907..a00965686 100644
--- a/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
+++ b/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
@@ -194,7 +194,7 @@
" mem_cells = cells # avoid setting twice\n",
" print(\"Memory cells set from file: {}\".format(cells))\n",
" \n",
- " f = h5py.File(fname, 'r', driver='core')\n",
+ " f = h5py.File(fname, 'r')\n",
" if rawversion == 2:\n",
" count = np.squeeze(f[\"/INDEX/{}/DET/{}CH0:xtdf/image/count\".format(karabo_id, channel)]) \n",
" bursts_per_file.append(np.count_nonzero(count))\n",
diff --git a/notebooks/AGIPD/playground/AGIPD-Gain_Distributions.ipynb b/notebooks/AGIPD/playground/AGIPD-Gain_Distributions.ipynb
index b32c92dc8..c01346307 100644
--- a/notebooks/AGIPD/playground/AGIPD-Gain_Distributions.ipynb
+++ b/notebooks/AGIPD/playground/AGIPD-Gain_Distributions.ipynb
@@ -151,7 +151,7 @@
" module, file = mf\n",
" infile = None\n",
" try:\n",
- " infile = h5py.File(file, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(file, \"r\")\n",
" gains = infile[\"/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/gain\".format(module)][()]\n",
" images = infile[\"/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/data\".format(module)][()]\n",
" cells = infile[\"/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/cellId\".format(module)][()]\n",
diff --git a/notebooks/AGIPD/playground/AGIPD_SingleM_test_Dark.ipynb b/notebooks/AGIPD/playground/AGIPD_SingleM_test_Dark.ipynb
index 533d0f36e..1e10696d0 100644
--- a/notebooks/AGIPD/playground/AGIPD_SingleM_test_Dark.ipynb
+++ b/notebooks/AGIPD/playground/AGIPD_SingleM_test_Dark.ipynb
@@ -263,7 +263,7 @@
" thresholds_offset_hard = thresholds_offset[gg]\n",
" thresholds_noise_hard = thresholds_noise[gg]\n",
" \n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" count = np.squeeze(infile[f\"/INDEX/{loc}/DET/{channel}CH0:xtdf/image/count\"])\n",
" first = np.squeeze(infile[f\"/INDEX/{loc}/DET/{channel}CH0:xtdf/image/first\"])\n",
"\n",
diff --git a/notebooks/AGIPD/playground/Characterize_AGIPD_CI.ipynb b/notebooks/AGIPD/playground/Characterize_AGIPD_CI.ipynb
index e52e43388..2809e3bc2 100644
--- a/notebooks/AGIPD/playground/Characterize_AGIPD_CI.ipynb
+++ b/notebooks/AGIPD/playground/Characterize_AGIPD_CI.ipynb
@@ -152,7 +152,7 @@
" fname = path_tmpl.format(path, mod, temp_p, mod, asic)\n",
" f = None\n",
" try:\n",
- " f = h5py.File(fname, \"r\", driver=\"core\")\n",
+ " f = h5py.File(fname, \"r\")\n",
" offset = f[\"/offset/mean\"]\n",
" offset = np.moveaxis(offset, 0, 3)\n",
" offsets.append(offset)\n",
diff --git a/notebooks/AGIPD/playground/Characterize_AGIPD_Dark-batch.ipynb b/notebooks/AGIPD/playground/Characterize_AGIPD_Dark-batch.ipynb
index 0f9d8caa2..d5db5d1cc 100644
--- a/notebooks/AGIPD/playground/Characterize_AGIPD_Dark-batch.ipynb
+++ b/notebooks/AGIPD/playground/Characterize_AGIPD_Dark-batch.ipynb
@@ -244,7 +244,7 @@
" \n",
" filename, filename_out, channel = inp\n",
"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" im = np.array(infile[\"/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/data\".format(channel)])\n",
" infile.close()\n",
"\n",
@@ -802,7 +802,7 @@
" fname = path_tmpl.format(path, mod, temp_p, mod, asic)\n",
" f = None\n",
" try:\n",
- " f = h5py.File(fname, \"r\", driver=\"core\")\n",
+ " f = h5py.File(fname, \"r\")\n",
" offset = f[\"/offset/mean\"]\n",
" offset = np.moveaxis(offset, 0, 3)\n",
" offsets.append(offset)\n",
diff --git a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_CompareXGM.ipynb b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_CompareXGM.ipynb
index 630e0ad15..99cf1769f 100644
--- a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_CompareXGM.ipynb
+++ b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_CompareXGM.ipynb
@@ -322,7 +322,7 @@
" def read_fun(filename, channel):\n",
" \"\"\" A reader function used by pyDetLib\n",
" \"\"\"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" count = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(channel)])\n",
" first = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/first\".format(channel)])\n",
" last_index = int(first[count != 0][-1]+count[count != 0][-1])\n",
diff --git a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_Darks.ipynb b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_Darks.ipynb
index 2b194138c..c727917ff 100644
--- a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_Darks.ipynb
+++ b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_Darks.ipynb
@@ -218,7 +218,7 @@
" filename, filename_out, channel = inp\n",
" thresholds_offset_hard, thresholds_offset_sigma, thresholds_noise_hard, thresholds_noise_sigma = bp_thresh \n",
"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" count = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(channel)])\n",
" first = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/first\".format(channel)])\n",
" last_index = int(first[count != 0][-1]+count[count != 0][-1])\n",
diff --git a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields.ipynb b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields.ipynb
index 6c30947e3..6f85912b2 100644
--- a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields.ipynb
+++ b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields.ipynb
@@ -268,7 +268,7 @@
" def read_fun(filename, channel):\n",
" \"\"\" A reader function used by pyDetLib\n",
" \"\"\"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" count = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(channel)])\n",
" first = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/first\".format(channel)])\n",
" last_index = int(first[count != 0][-1]+count[count != 0][-1])\n",
@@ -442,7 +442,7 @@
" def read_fun(filename, channel):\n",
" \"\"\" A reader function used by pyDetLib\n",
" \"\"\"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" count = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(channel)])\n",
" first = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/first\".format(channel)])\n",
" last_index = int(first[count != 0][-1]+count[count != 0][-1])\n",
@@ -951,7 +951,7 @@
" block_size = [64, 64]\n",
" def read_fun(filename, channel):\n",
" \n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" count = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(channel)])\n",
" first = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/first\".format(channel)])\n",
" last_index = int(first[count != 0][-1]+count[count != 0][-1])\n",
diff --git a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields_Coupling.ipynb b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields_Coupling.ipynb
index 738892f6a..5fb264609 100644
--- a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields_Coupling.ipynb
+++ b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields_Coupling.ipynb
@@ -166,7 +166,7 @@
" def read_fun(filename, channel):\n",
" \"\"\" A reader function used by pyDetLib\n",
" \"\"\"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" status = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/status\".format(channel)])\n",
" last = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/last\".format(channel)])\n",
" last_index = int(last[status != 0][-1])\n",
diff --git a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb
index 49c2e334f..eb1807e2a 100644
--- a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb
+++ b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb
@@ -452,7 +452,7 @@
" def read_fun(filename, channel):\n",
" \"\"\" A reader function used by pyDetLib\n",
" \"\"\"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" if rawversion == 2:\n",
" count = np.squeeze(infile[\"/INDEX/{}_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(instrument, channel)])\n",
" first = np.squeeze(infile[\"/INDEX/{}_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/first\".format(instrument, channel)])\n",
@@ -697,7 +697,7 @@
" def read_fun(filename, channel):\n",
" \"\"\" A reader function used by pyDetLib\n",
" \"\"\"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" if rawversion == 2:\n",
" count = np.squeeze(infile[\"/INDEX/{}_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(instrument, channel)])\n",
" first = np.squeeze(infile[\"/INDEX/{}_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/first\".format(instrument, channel)])\n",
@@ -1293,7 +1293,7 @@
" \n",
" def read_fun(filename, channel):\n",
" \n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" if rawversion == 2:\n",
" count = np.squeeze(infile[\"/INDEX/{}_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(instrument, channel)])\n",
" first = np.squeeze(infile[\"/INDEX/{}_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/first\".format(instrument, channel)])\n",
diff --git a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_Transition.ipynb b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_Transition.ipynb
index 846c32ee6..6629bd819 100644
--- a/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_Transition.ipynb
+++ b/notebooks/AGIPD/playground/Characterize_AGIPD_Gain_Transition.ipynb
@@ -169,7 +169,7 @@
" \"\"\" A reader function used by pyDetLib\n",
" \"\"\"\n",
" \n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" \n",
" imarr = infile[\"/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/data\".format(channel)]\n",
" im = np.array(imarr)\n",
@@ -257,7 +257,7 @@
" \"\"\" A reader function used by pyDetLib\n",
" \"\"\"\n",
" \n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" \n",
" imarr = infile[\"/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/data\".format(channel)]\n",
" im = np.array(imarr)\n",
diff --git a/notebooks/AGIPD/playground/Characterize_AGIPD_Pulse_Cell.ipynb b/notebooks/AGIPD/playground/Characterize_AGIPD_Pulse_Cell.ipynb
index 12e85c75e..88604b13e 100644
--- a/notebooks/AGIPD/playground/Characterize_AGIPD_Pulse_Cell.ipynb
+++ b/notebooks/AGIPD/playground/Characterize_AGIPD_Pulse_Cell.ipynb
@@ -128,7 +128,7 @@
" def read_fun(filename, channel):\n",
" \"\"\" A reader function used by pyDetLib\n",
" \"\"\"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" im = np.array(infile[\"/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/data\".format(channel)][trains[0]*memory_cells:trains[1]*memory_cells,...]) \n",
" carr = infile[\"/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/cellId\".format(channel)][trains[0]*memory_cells:trains[1]*memory_cells]\n",
" cells = np.squeeze(np.array(carr))\n",
@@ -296,7 +296,7 @@
" def read_fun(filename, channel):\n",
" \"\"\" A reader function used by pyDetLib\n",
" \"\"\"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" status = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/status\".format(channel)])\n",
" last = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/last\".format(channel)])\n",
" last_index = int(last[status != 0][-1])\n",
@@ -563,7 +563,7 @@
" block_size = [64, 64]\n",
" def read_fun(filename, channel):\n",
" \n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" status = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/status\".format(channel)])\n",
" last = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/last\".format(channel)])\n",
" last_index = int(last[status != 0][-1])\n",
diff --git a/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC.ipynb b/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC.ipynb
index 9ab481738..f26d156ec 100644
--- a/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC.ipynb
+++ b/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC.ipynb
@@ -129,7 +129,7 @@
" fname = os.path.join(path_temp.format(run),\n",
" image_name_temp.format(run, channel, seq))\n",
" print('Reading ',fname)\n",
- " f = h5py.File(fname, 'r', driver='core')\n",
+ " f = h5py.File(fname, 'r')\n",
" \n",
" count = np.squeeze(f[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(channel)])\n",
" f.close()\n",
@@ -204,7 +204,7 @@
" cfac = 2 if il_mode else 1\n",
" def read_raw_data_file(fname, channel, cells = cells, cells_tot = cells, bursts = 250,\n",
" skip_first_burst = True, first_burst_length = cells):\n",
- " f = h5py.File(fname, 'r', driver='core')\n",
+ " f = h5py.File(fname, 'r')\n",
" #print('Reading ',fname)\n",
" image_path_temp = 'INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/data'\n",
" cellID_path_temp = 'INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/cellId'\n",
diff --git a/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC_KMeans.ipynb b/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC_KMeans.ipynb
index cae7976f7..d84131d76 100644
--- a/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC_KMeans.ipynb
+++ b/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC_KMeans.ipynb
@@ -159,7 +159,7 @@
" \n",
" def read_raw_data_file(fname, channel, cells = 64, cells_tot = 64, bursts = 250,\n",
" skip_first_burst = True, first_burst_length = 64):\n",
- " f = h5py.File(fname, 'r', driver='core')\n",
+ " f = h5py.File(fname, 'r')\n",
" print('Reading ',fname)\n",
" image_path_temp = 'INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/data'\n",
" cellID_path_temp = 'INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/cellId'\n",
diff --git a/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC_mlearn.ipynb b/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC_mlearn.ipynb
index 831dc4bd2..22e9fb728 100644
--- a/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC_mlearn.ipynb
+++ b/notebooks/AGIPD/playground/Chracterize_AGIPD_Gain_PC_mlearn.ipynb
@@ -162,7 +162,7 @@
" fname = os.path.join(path_temp.format(run),\n",
" image_name_temp.format(run, channel, seq))\n",
" print('Reading ',fname)\n",
- " f = h5py.File(fname, 'r', driver='core')\n",
+ " f = h5py.File(fname, 'r')\n",
" if rawversion == 2:\n",
" count = np.squeeze(f[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(channel)]) \n",
" bursts_per_file.append(np.count_nonzero(count))\n",
@@ -196,7 +196,7 @@
" \n",
" def read_raw_data_file(fname, channel, cells = cells, cells_tot = cells, bursts = 250,\n",
" skip_first_burst = True, first_burst_length = cells):\n",
- " f = h5py.File(fname, 'r', driver='core')\n",
+ " f = h5py.File(fname, 'r')\n",
" \n",
" #print('Reading ',fname)\n",
" image_path_temp = 'INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/data'\n",
diff --git a/notebooks/AGIPD/playground/Correct_AGIPD-Verify.ipynb b/notebooks/AGIPD/playground/Correct_AGIPD-Verify.ipynb
index 1869958cc..08c8d0825 100644
--- a/notebooks/AGIPD/playground/Correct_AGIPD-Verify.ipynb
+++ b/notebooks/AGIPD/playground/Correct_AGIPD-Verify.ipynb
@@ -314,7 +314,7 @@
" \n",
" filename, filename_out, channel, offset, base_offset, rel_gain, threshold, mask, mgh = inp\n",
"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" count = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/count\".format(channel)])\n",
" first = np.squeeze(infile[\"/INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/first\".format(channel)])\n",
" last_index = int(first[count != 0][-1]+count[count != 0][-1])\n",
@@ -333,7 +333,7 @@
" dont_copy = [\"INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/{}\".format(channel, do)\n",
" for do in dont_copy]\n",
"\n",
- " outfile = h5py.File(filename_out, \"w\", driver=\"core\")\n",
+ " outfile = h5py.File(filename_out, \"w\")\n",
" def visitor(k, item):\n",
" if k not in dont_copy:\n",
" if isinstance(item, h5py.Group):\n",
diff --git a/notebooks/AGIPD/playground/Correct_AGIPD-batch.ipynb b/notebooks/AGIPD/playground/Correct_AGIPD-batch.ipynb
index 92daf90ca..2a9afd114 100644
--- a/notebooks/AGIPD/playground/Correct_AGIPD-batch.ipynb
+++ b/notebooks/AGIPD/playground/Correct_AGIPD-batch.ipynb
@@ -193,7 +193,7 @@
" \n",
" filename, filename_out, channel, offset, base_offset, rel_gain, threshold, mask = inp\n",
"\n",
- " infile = h5py.File(filename, \"r\", driver=\"core\")\n",
+ " infile = h5py.File(filename, \"r\")\n",
" im = np.array(infile[\"/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/data\".format(channel)])\n",
"\n",
" cellid = np.array(infile[\"/INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/cellId\".format(channel)])\n",
@@ -206,7 +206,7 @@
" dont_copy = [\"INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/image/{}\".format(channel, do)\n",
" for do in dont_copy]\n",
"\n",
- " outfile = h5py.File(filename_out, \"w\", driver=\"core\")\n",
+ " outfile = h5py.File(filename_out, \"w\")\n",
" def visitor(k, item):\n",
" if k not in dont_copy:\n",
" if isinstance(item, h5py.Group):\n",
--
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