diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
index c97abbb92ac04152700614ac0f28affca9a53fca..481c8dfb440b1cdb1599a4c9b097f50d43feb36e 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
@@ -25,15 +25,15 @@
"outputs": [],
"source": [
"cluster_profile = \"noDB\" # The ipcluster profile to use\n",
- "in_folder = \"/gpfs/exfel/d/raw/SPB/202030/p900138\" # path to input data, required\n",
- "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/AGIPDbad_sep64\" # path to output to, required\n",
+ "in_folder = \"/gpfs/exfel/d/raw/DETLAB/202031/p900172/\" # path to input data, required\n",
+ "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/miniHalfAGIPD\" # path to output to, required\n",
"sequences = [0] # sequence files to evaluate.\n",
"modules = [-1] # list of modules to evaluate, RANGE ALLOWED\n",
- "run_high = 167 # run number in which high gain data was recorded, required\n",
- "run_med = 168 # run number in which medium gain data was recorded, required\n",
- "run_low = 169 # run number in which low gain data was recorded, required\n",
+ "run_high = 84 # run number in which high gain data was recorded, required\n",
+ "run_med = 87 # run number in which medium gain data was recorded, required\n",
+ "run_low = 88 # run number in which low gain data was recorded, required\n",
"\n",
- "karabo_id = \"SPB_DET_AGIPD1M-1\" # karabo karabo_id\n",
+ "karabo_id = \"DETLAB_DET_AGIPD500K2G\" # karabo karabo_id\n",
"karabo_da = ['-1'] # a list of data aggregators names, Default [-1] for selecting all data aggregators\n",
"receiver_id = \"{}CH0\" # inset for receiver devices\n",
"path_template = 'RAW-R{:04d}-{}-S{:05d}.h5' # the template to use to access data\n",
@@ -51,8 +51,8 @@
"\n",
"mem_cells = 0 # number of memory cells used, set to 0 to automatically infer\n",
"bias_voltage = 300 # detector bias voltage\n",
- "gain_setting = 0.1 # the gain setting, use 0.1 to try to auto-determine\n",
- "acq_rate = 0. # the detector acquisition rate, use 0 to try to auto-determine\n",
+ "gain_setting = 0.0 # the gain setting, use 0.1 to try to auto-determine\n",
+ "acq_rate = 1.1 # the detector acquisition rate, use 0 to try to auto-determine\n",
"interlaced = False # assume interlaced data format, for data prior to Dec. 2017\n",
"rawversion = 2 # RAW file format version\n",
"\n",
@@ -143,13 +143,19 @@
"cal_db_interface = get_random_db_interface(cal_db_interface)\n",
"print(f'Calibration database interface: {cal_db_interface}')\n",
"\n",
- "loc = None\n",
"instrument = karabo_id.split(\"_\")[0]\n",
+ "\n",
"if instrument == \"SPB\":\n",
" dinstance = \"AGIPD1M1\"\n",
- "else:\n",
+ " nmods = 16\n",
+ "elif instrument == \"MID\":\n",
" dinstance = \"AGIPD1M2\"\n",
- " \n",
+ " nmods = 16\n",
+ "# TODO: Remove DETLAB\n",
+ "elif instrument == \"HED\" or instrument == \"DETLAB\":\n",
+ " dinstance = \"AGIPD500K\"\n",
+ " nmods = 8\n",
+ "\n",
"control_names = ['{}/r{:04d}/RAW-R{:04d}-{}-S00000.h5'.format(in_folder, r, r, karabo_da_control)\n",
" for r in (run_high, run_med, run_low)] \n",
"\n",
@@ -167,7 +173,6 @@
"metadata": {},
"outputs": [],
"source": [
- "gain_names = ['High', 'Medium', 'Low']\n",
"runs = [run_high, run_med, run_low]\n",
"\n",
"if \"{\" in h5path_ctrl:\n",
@@ -210,7 +215,7 @@
"source": [
"if karabo_da[0] == '-1':\n",
" if modules[0] == -1:\n",
- " modules = list(range(16))\n",
+ " modules = list(range(nmods))\n",
" karabo_da = [\"AGIPD{:02d}\".format(i) for i in modules]\n",
"else:\n",
" modules = [int(x[-2:]) for x in karabo_da]\n",
@@ -286,6 +291,8 @@
" acq_rate: float,\n",
" h5path: str,\n",
" h5path_idx: str,\n",
+ " control_names: List[str],\n",
+ " karabo_id_control: str,\n",
" inp: Tuple[str, int, int]) -> Tuple[np.array, np.array, np.array, np.array, int, np.array, int, float]:\n",
" import numpy as np\n",
" import copy\n",
@@ -418,7 +425,8 @@
"p = partial(characterize_module, IL_MODE, max_cells,\n",
" (thresholds_offset_hard, thresholds_offset_sigma,\n",
" thresholds_noise_hard, thresholds_noise_sigma),\n",
- " rawversion, karabo_id, acq_rate, h5path, h5path_idx)\n",
+ " rawversion, karabo_id, acq_rate, h5path, h5path_idx,\n",
+ " control_names, karabo_id_control)\n",
"\n",
"# Don't remove. Used for Debugging.\n",
"#results = list(map(p, inp))\n",
@@ -622,12 +630,14 @@
},
"outputs": [],
"source": [
- "mnames=[]\n",
- "for i in modules:\n",
- " qm = f\"Q{i//4+1}M{i % 4+1}\"\n",
- " mnames.append(qm)\n",
- " display(Markdown(f'## Position of the module {qm} and it\\'s ASICs##'))\n",
- "show_processed_modules(dinstance, constants=None, mnames=mnames, mode=\"position\")"
+ "# TODO: add show_processed_modules diagram for Mini-Half AGIPD\n",
+ "if dinstance != \"AGIPD500K\":\n",
+ " mnames=[]\n",
+ " for i in modules:\n",
+ " qm = f\"Q{i//4+1}M{i % 4+1}\"\n",
+ " mnames.append(qm)\n",
+ " display(Markdown(f'## Position of the module {qm} and it\\'s ASICs##'))\n",
+ " show_processed_modules(dinstance, constants=None, mnames=mnames, mode=\"position\")"
]
},
{
diff --git a/notebooks/generic/overallmodules_Darks_Summary_NBC.ipynb b/notebooks/generic/overallmodules_Darks_Summary_NBC.ipynb
index bacf630eaf9b0c4b61d0773ddd8c33d0d7310150..a40e1281c649d3625d1d65da961f0c2b0e00efdd 100644
--- a/notebooks/generic/overallmodules_Darks_Summary_NBC.ipynb
+++ b/notebooks/generic/overallmodules_Darks_Summary_NBC.ipynb
@@ -9,9 +9,8 @@
"#Author: K. Ahmed, M. Karnevsky, Version: 0.1\n",
"#The following is a summary for the processing of dark images and calibration constants production.\n",
"\n",
- "cluster_profile = \"noDB\" # The ipcluster profile to use\n",
- "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/agipd-test-report\" # path to output to, required\n",
- "karabo_id = \"SPB_DET_AGIPDM-1\" # detector instance\n",
+ "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/miniHalfAGIPD\" # path to output to, required\n",
+ "karabo_id = \"DETLAB_DET_AGIPD500K2G\" # detector instance\n",
"gain_names = ['High gain', 'Medium gain', 'Low gain'] # a list of gain names to be used in plotting\n",
"threshold_names = ['HG-MG threshold', 'MG_LG threshold'] # a list of gain names to be used in plotting"
]
@@ -54,12 +53,17 @@
"metadata": {},
"outputs": [],
"source": [
- "SHOW=True\n",
"if \"AGIPD\" in karabo_id:\n",
" if \"SPB\" in karabo_id:\n",
" dinstance = \"AGIPD1M1\"\n",
+ " nmod = 16\n",
+ " qm = f\"Q{i//4+1}M{i%4+1}\"\n",
" elif \"MID\" in karabo_id:\n",
" dinstance = \"AGIPD1M2\"\n",
+ " nmod = 16\n",
+ " elif \"HED\" in karabo_id or \"DETLAB\" in karabo_id :\n",
+ " dinstance = \"AGIPD500K\"\n",
+ " nmod = 8\n",
" display(Markdown(\"\"\"\n",
" \n",
"# Summary of AGIPD dark characterization #\n",
@@ -112,6 +116,7 @@
" \n",
"elif \"LPD\" in karabo_id:\n",
" dinstance = \"LPD1M1\"\n",
+ " nmod = 16\n",
" display(Markdown(\"\"\"\n",
" \n",
"# Summary of LPD dark characterization #\n",
@@ -154,6 +159,7 @@
"\"\"\"))\n",
"elif \"DSSC\" in karabo_id:\n",
" dinstance = \"DSSC1M1\"\n",
+ " nmod = 16\n",
" display(Markdown(\"\"\"\n",
" \n",
"# Summary of DSSC dark characterization #\n",
@@ -180,7 +186,7 @@
"old_cons = OrderedDict()\n",
"mod_names = []\n",
"# Loop over modules\n",
- "for i in range(16):\n",
+ "for i in range(nmod):\n",
" qm = f\"Q{i//4+1}M{i%4+1}\"\n",
" # loop over constants\n",
" detinst = getattr(Detectors, dinstance)\n",
@@ -247,8 +253,10 @@
},
"outputs": [],
"source": [
- "display(Markdown('## Processed modules ##'))\n",
- "show_processed_modules(dinstance, constants, mod_names, mode=\"processed\")"
+ "# TODO: add show_processed_modules diagram for Mini-Half AGIPD\n",
+ "if dinstance != \"AGIPD500K\":\n",
+ " display(Markdown('## Processed modules ##'))\n",
+ " show_processed_modules(dinstance, constants, mod_names, mode=\"processed\")"
]
},
{
@@ -297,6 +305,14 @@
"gainstages = 1\n",
"\n",
"for const_name, const in constants.items():\n",
+ " \n",
+ " \n",
+ " #TODO: add a Summary figure across modules\n",
+ " if dinstance == \"AGIPD500K\":\n",
+ " display(Markdown(f'WARNING: No summary figures are available for AGIPD mini-half at the moment.'))\n",
+ " break\n",
+ " \n",
+ " \n",
" if const_name == 'BadPixelsDark':\n",
" continue\n",
" # Check if constant gain available in constant e.g. AGIPD, LPD\n",
@@ -317,8 +333,8 @@
" glabel = threshold_names\n",
" else:\n",
" glabel = gain_names\n",
- " for i in range(16):\n",
- " qm = f\"Q{i//4+1}M{i%4+1}\"\n",
+ " for i in range(nmods):\n",
+ " qm = qm.format(i)\n",
" if qm in mod_names:\n",
" m_idx = mod_names.index(qm)\n",
" # Check if constant shape of 5 indices e.g. AGIPD, LPD\n",
@@ -550,6 +566,20 @@
" md = display(Latex(tabulate.tabulate(\n",
" table, tablefmt='latex', headers=header)))"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
}
],
"metadata": {