From de94a3041e891222f3110047d0c56e7fe3060c58 Mon Sep 17 00:00:00 2001
From: David Hammer <dhammer@mailbox.org>
Date: Thu, 25 Feb 2021 13:57:22 +0100
Subject: [PATCH] Additional refactoring
---
.../Characterize_AGIPD_Gain_Darks_NBC.ipynb | 72 +++++++++++--------
1 file changed, 41 insertions(+), 31 deletions(-)
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
index dfab44ce1..4672a39e2 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
@@ -117,7 +117,6 @@
"source": [
"gains = np.arange(3)\n",
"\n",
- "IL_MODE = interlaced\n",
"max_cells = mem_cells\n",
" \n",
"offset_runs = OrderedDict()\n",
@@ -127,7 +126,7 @@
"\n",
"creation_time=None\n",
"if use_dir_creation_date:\n",
- " creation_time = get_dir_creation_date(in_folder, run_high, verbosity=2)\n",
+ " creation_time = get_dir_creation_date(in_folder, run_high)\n",
"\n",
"print(f\"Using {creation_time} as creation time of constant.\")\n",
"\n",
@@ -165,8 +164,8 @@
"source": [
"runs = [run_high, run_med, run_low]\n",
"\n",
- "if \"{\" in h5path_ctrl:\n",
- " h5path_ctrl = h5path_ctrl.format(karabo_id_control)\n",
+ "# insert control device if format string (does nothing otherwise)\n",
+ "h5path_ctrl = h5path_ctrl.format(karabo_id_control)\n",
"\n",
"if gain_setting == 0.1:\n",
" if creation_time.replace(tzinfo=None) < dateutil.parser.parse('2020-01-31'):\n",
@@ -218,7 +217,7 @@
"print(f\"Memory cells: {mem_cells}/{max_cells}\")\n",
"print(\"Runs: {}\".format([ v for v in offset_runs.values()]))\n",
"print(f\"Sequences: {sequences}\")\n",
- "print(f\"Interlaced mode: {IL_MODE}\")\n",
+ "print(f\"Interlaced mode: {interlaced}\")\n",
"print(f\"Using DB: {db_output}\")\n",
"print(f\"Input: {in_folder}\")\n",
"print(f\"Output: {out_folder}\")\n",
@@ -246,6 +245,16 @@
"print(f\"Will process a total of {total_sequences} files.\")"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def index_to_qm(i: int):\n",
+ " return f\"Q{i//4+1}M{i%4+1}\""
+ ]
+ },
{
"cell_type": "markdown",
"metadata": {},
@@ -261,9 +270,24 @@
"metadata": {},
"outputs": [],
"source": [
- "def characterize_module(inp: Tuple[str, int, int]) -> Tuple[np.array, np.array, np.array, np.array, int, np.array, int, float]:\n",
- " fast_data_filename, channel, gg = inp\n",
+ "if thresholds_offset_hard == [0, 0]:\n",
+ " thresholds_offset_hard = [thresholds_offset_hard_hg, thresholds_offset_hard_mg, thresholds_offset_hard_lg]\n",
+ "else:\n",
+ " thresholds_offset_hard = [thresholds_offset_hard] * 3\n",
"\n",
+ "if thresholds_noise_hard == [0, 0]:\n",
+ " thresholds_noise_hard = [thresholds_noise_hard_hg, thresholds_noise_hard_mg, thresholds_noise_hard_lg]\n",
+ "else:\n",
+ " thresholds_noise_hard = [thresholds_noise_hard] * 3"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def characterize_module(fast_data_filename: str, channel: int, gg: int) -> Tuple[np.array, np.array, np.array, np.array, int, np.array, int, float]:\n",
" if max_cells == 0:\n",
" num_cells = get_num_cells(fast_data_filename, karabo_id, channel)\n",
" else:\n",
@@ -301,7 +325,7 @@
" im = np.array(infile[f\"{h5path_f}/data\"][first_index:last_index,...])\n",
" cellIds = np.squeeze(infile[f\"{h5path_f}/cellId\"][first_index:last_index,...])\n",
"\n",
- " if IL_MODE:\n",
+ " if interlaced:\n",
" ga = im[1::2, 0, ...]\n",
" im = im[0::2, 0, ...].astype(np.float32)\n",
" cellIds = cellIds[::2]\n",
@@ -349,33 +373,22 @@
"\n",
" return offset, noise, gains, gains_std, gg, bp, num_cells, local_acq_rate\n",
"\n",
+ "\n",
"offset_g = OrderedDict()\n",
"noise_g = OrderedDict()\n",
"gain_g = OrderedDict()\n",
"gainstd_g = OrderedDict()\n",
"badpix_g = OrderedDict()\n",
- "gg = 0\n",
"\n",
"start = datetime.now()\n",
"all_cells = []\n",
"all_acq_rate = []\n",
"\n",
- "if thresholds_offset_hard == [0, 0]:\n",
- " thresholds_offset_hard = [thresholds_offset_hard_hg, thresholds_offset_hard_mg, thresholds_offset_hard_lg]\n",
- "else:\n",
- " thresholds_offset_hard = [thresholds_offset_hard] * 3\n",
- "\n",
- "if thresholds_noise_hard == [0, 0]:\n",
- " thresholds_noise_hard = [thresholds_noise_hard_hg, thresholds_noise_hard_mg, thresholds_noise_hard_lg]\n",
- "else:\n",
- " thresholds_noise_hard = [thresholds_noise_hard] * 3\n",
- "\n",
- "\n",
"inp = []\n",
- "for gain, mapped_files in gain_mapped_files.items():\n",
+ "for gg, (gain, mapped_files) in enumerate(gain_mapped_files.items()):\n",
" dones = []\n",
" for i in modules:\n",
- " qm = f\"Q{i//4+1}M{i%4+1}\"\n",
+ " qm = index_to_qm(i)\n",
" if qm in mapped_files and not mapped_files[qm].empty():\n",
" fname_in = mapped_files[qm].get()\n",
" print(\"Process file: \", fname_in)\n",
@@ -384,17 +397,14 @@
" continue\n",
" inp.append((fname_in, i, gg))\n",
"\n",
- " gg += 1\n",
- "\n",
"with multiprocessing.Pool() as pool:\n",
- " results = pool.map(characterize_module, inp)\n",
+ " results = pool.starmap(characterize_module, inp)\n",
"\n",
- "for ii, r in enumerate(results):\n",
- " offset, noise, gains, gains_std, gg, bp, thiscell, thisacq = r\n",
+ "for offset, noise, gains, gains_std, gg, bp, thiscell, thisacq in results:\n",
" all_cells.append(thiscell)\n",
" all_acq_rate.append(thisacq)\n",
" for i in modules:\n",
- " qm = f\"Q{i//4+1}M{i%4+1}\"\n",
+ " qm = index_to_qm(i)\n",
" if qm not in offset_g:\n",
" offset_g[qm] = np.zeros((offset.shape[0], offset.shape[1], offset.shape[2], 3))\n",
" noise_g[qm] = np.zeros_like(offset_g[qm])\n",
@@ -461,7 +471,7 @@
"source": [
"res = OrderedDict()\n",
"for i in modules:\n",
- " qm = \"Q{}M{}\".format(i//4+1, i%4+1)\n",
+ " qm = index_to_qm(i)\n",
" res[qm] = {'Offset': offset_g[qm],\n",
" 'Noise': noise_g[qm],\n",
" 'ThresholdsDark': thresholds_g[qm],\n",
@@ -492,7 +502,7 @@
"# Create the modules dict of karabo_das and PDUs\n",
"qm_dict = OrderedDict()\n",
"for i, k_da in zip(modules, karabo_da):\n",
- " qm = f\"Q{i//4+1}M{i%4+1}\"\n",
+ " qm = index_to_qm(i)\n",
" qm_dict[qm] = {\"karabo_da\": k_da,\n",
" \"db_module\": \"\"}"
]
@@ -596,7 +606,7 @@
"source": [
"mnames=[]\n",
"for i in modules:\n",
- " qm = f\"Q{i//4+1}M{i % 4+1}\"\n",
+ " qm = index_to_qm(i)\n",
" mnames.append(qm)\n",
" display(Markdown(f'## Position of the module {qm} and its ASICs##'))\n",
"show_processed_modules(dinstance, constants=None, mnames=mnames, mode=\"position\")"
--
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