From abd3f4cf9346ea961185286cb246a37ee99c2a3b Mon Sep 17 00:00:00 2001
From: David Hammer <dhammer@mailbox.org>
Date: Wed, 7 Apr 2021 13:48:06 +0200
Subject: [PATCH] Recreating showcase of threads for cell processing
---
.../Characterize_AGIPD_Gain_Darks_NBC.ipynb | 44 ++++++++++++-------
setup.py | 1 +
2 files changed, 28 insertions(+), 17 deletions(-)
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
index 722eb0a11..460585328 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
@@ -86,6 +86,7 @@
"import h5py\n",
"import matplotlib\n",
"import numpy as np\n",
+ "import pasha as psh\n",
"import tabulate\n",
"import yaml\n",
"\n",
@@ -104,9 +105,7 @@
" get_gain_setting,\n",
" get_num_cells,\n",
")\n",
- "\n",
"from cal_tools.enums import AgipdGainMode, BadPixels\n",
- "\n",
"from cal_tools.plotting import (\n",
" create_constant_overview,\n",
" plot_badpix_3d,\n",
@@ -381,23 +380,26 @@
" ga = np.rollaxis(ga, 2)\n",
" ga = np.rollaxis(ga, 2, 1)\n",
" \n",
- " offset = np.zeros((im.shape[0], im.shape[1], num_cells))\n",
- " noise = np.zeros((im.shape[0], im.shape[1], num_cells))\n",
+ " offset = psh.array((im.shape[0], im.shape[1], num_cells))\n",
+ " noise = psh.array((im.shape[0], im.shape[1], num_cells))\n",
"\n",
" if fixed_gain_mode:\n",
" gains = None\n",
" gains_std = None\n",
" else:\n",
- " gains = np.zeros((im.shape[0], im.shape[1], num_cells))\n",
- " gains_std = np.zeros((im.shape[0], im.shape[1], num_cells))\n",
- "\n",
- " for cc in np.unique(cellIds[cellIds < num_cells]):\n",
- " cellidx = cellIds == cc\n",
- " offset[...,cc] = np.median(im[..., cellidx], axis=2)\n",
- " noise[...,cc] = np.std(im[..., cellidx], axis=2)\n",
+ " gains = psh.array((im.shape[0], im.shape[1], num_cells))\n",
+ " gains_std = psh.array((im.shape[0], im.shape[1], num_cells))\n",
+ "\n",
+ " def process_cell(worker_id, array_index, cell_number):\n",
+ " cell_slice_index = (cellIds == cell_number)\n",
+ " im_slice = im[..., cell_slice_index]\n",
+ " offset[..., cell_number] = np.median(im_slice, axis=2)\n",
+ " noise[..., cell_number] = np.std(im_slice, axis=2)\n",
" if not fixed_gain_mode:\n",
- " gains[...,cc] = np.median(ga[..., cellidx], axis=2)\n",
- " gains_std[...,cc] = np.std(ga[..., cellidx], axis=2)\n",
+ " ga_slice = ga[..., cell_slice_index]\n",
+ " gains[..., cell_number] = np.median(ga_slice, axis=2)\n",
+ " gains_std[..., cell_number] = np.std(ga_slice, axis=2)\n",
+ " psh.map(process_cell, np.arange(num_cells))\n",
"\n",
" # bad pixels\n",
" bp = np.zeros(offset.shape, np.uint32)\n",
@@ -422,6 +424,17 @@
" return offset, noise, gains, gains_std, gg, bp, num_cells, local_acq_rate"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "parallel_num_procs = 4\n",
+ "parallel_num_threads = multiprocessing.cpu_count() // parallel_num_procs\n",
+ "psh.set_default_context(\"threads\", num_workers=parallel_num_threads)"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -435,7 +448,6 @@
" gain_g = OrderedDict()\n",
" gainstd_g = OrderedDict()\n",
" \n",
- "start = datetime.now()\n",
"all_cells = []\n",
"all_acq_rate = []\n",
"\n",
@@ -452,7 +464,7 @@
" continue\n",
" inp.append((fname_in, i, gg))\n",
"\n",
- "with multiprocessing.Pool() as pool:\n",
+ "with multiprocessing.Pool(processes=parallel_num_procs) as pool:\n",
" results = pool.starmap(characterize_module, inp)\n",
"\n",
"for offset, noise, gains, gains_std, gg, bp, thiscell, thisacq in results:\n",
@@ -476,8 +488,6 @@
" gainstd_g[qm][..., gg] = gains_std\n",
"\n",
"\n",
- "duration = (datetime.now() - start).total_seconds()\n",
- "\n",
"max_cells = np.max(all_cells)\n",
"print(f\"Using {max_cells} memory cells\")\n",
"acq_rate = np.max(all_acq_rate)\n",
diff --git a/setup.py b/setup.py
index e506c721b..f5b32c6bd 100644
--- a/setup.py
+++ b/setup.py
@@ -76,6 +76,7 @@ setup(
"iCalibrationDB @ git+ssh://git@git.xfel.eu:10022/detectors/cal_db_interactive.git@2.0.5", # noqa
"nbparameterise @ git+ssh://git@git.xfel.eu:10022/detectors/nbparameterise.git@0.3", # noqa
"XFELDetectorAnalysis @ git+ssh://git@git.xfel.eu:10022/karaboDevices/pyDetLib.git@2.5.6-2.10.0#subdirectory=lib", # noqa
+ "pasha @ git+https://github.com/European-XFEL/pasha.git",
"Cython==0.29.21",
"Jinja2==2.11.2",
"astcheck==0.2.5",
--
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