diff --git a/notebooks/Gotthard2/Characterize_Darks_Gotthard2_NBC.ipynb b/notebooks/Gotthard2/Characterize_Darks_Gotthard2_NBC.ipynb
index ee6e5c160964ce530ecc99fae80ff6b7ea362039..fbd93209f6fbd32753332082808d8ae70e005769 100644
--- a/notebooks/Gotthard2/Characterize_Darks_Gotthard2_NBC.ipynb
+++ b/notebooks/Gotthard2/Characterize_Darks_Gotthard2_NBC.ipynb
@@ -102,20 +102,15 @@
"run_nums = [run_high, run_med, run_low]\n",
"in_folder = Path(in_folder)\n",
"out_folder = Path(out_folder)\n",
- "out_folder.mkdir(exist_ok=True)\n",
- "\n",
+ "out_folder.mkdir(parents=True, exist_ok=True)\n",
"print(f\"Process modules: {karabo_da}\")\n",
"\n",
- "run_dc = RunDirectory(in_folder / f\"r{run_high:04d}\")\n",
- "file_loc = f\"proposal:{run_dc.run_metadata()['proposalNumber']} runs:{run_high} {run_med} {run_low}\" # noqa\n",
- "\n",
- "instrument_src = instrument_source_template.format(karabo_id, receiver_template)\n",
"ctrl_src = ctrl_source_template.format(karabo_id_control, control_template)\n",
"\n",
"# Read report path to associate it later with injected constants.\n",
"report = get_report(out_folder)\n",
"\n",
- "\n",
+ "creation_time = None\n",
"if overwrite_creation_time:\n",
" creation_time = datetime.datetime.strptime(\n",
" overwrite_creation_time, \"%Y-%m-%d %H:%M:%S.%f\"\n",
@@ -129,6 +124,19 @@
" karabo_id_control = karabo_id"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "c176a86f",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "run_dc = RunDirectory(in_folder / f\"r{run_high:04d}\")\n",
+ "file_loc = f\"proposal:{run_dc.run_metadata()['proposalNumber']} runs:{run_high} {run_med} {run_low}\" # noqa\n",
+ "\n",
+ "receivers = list(run_dc.select(f'{karabo_id}/DET/{receiver_template}*').all_sources)"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -193,7 +201,15 @@
"single_photon = conditions[\"single_photon\"].pop()\n",
"print(\"Single photon: \", single_photon)\n",
"acquisition_rate = conditions[\"acquisition_rate\"].pop()\n",
- "print(\"Acquisition rate: \", acquisition_rate)"
+ "print(\"Acquisition rate: \", acquisition_rate)\n",
+ "\n",
+ "# Decide if GH2 is 25um or 50um\n",
+ "gh2_hostname = run_dc.get_run_value(ctrl_src, \"rxHostname\")\n",
+ "# gh2_hostname is a vector of bytes objects.\n",
+ "# GH2 25um has two host-names unlike 50um which has one.\n",
+ "if gh2_hostname[1].decode(\"utf-8\"): # For 25um use virtual karabo_das for CALCAT data mapping.\n",
+ " karabo_da = [f\"{karabo_da[0]}/1\", f\"{karabo_da[0]}/2\"]\n",
+ " print(\"Processing 25um Gotthard2.\")"
]
},
{
@@ -204,9 +220,7 @@
"outputs": [],
"source": [
"def specify_trains_to_process(\n",
- " img_key_data: \"extra_data.KeyData\", # noqa\n",
- " max_trains: int = 0,\n",
- " min_trains: int = 0,\n",
+ " img_key_data: \"extra_data.KeyData\",\n",
"):\n",
" \"\"\"Specify total number of trains to process.\n",
" Based on given min_trains and max_trains, if given.\n",
@@ -218,7 +232,7 @@
" n_trains = img_key_data.shape[0]\n",
" all_trains = len(img_key_data.train_ids)\n",
" print(\n",
- " f\"{mod} has {all_trains - n_trains} \"\n",
+ " f\"{receiver} has {all_trains - n_trains} \"\n",
" f\"trains with empty frames out of {all_trains} trains\"\n",
" )\n",
"\n",
@@ -272,7 +286,7 @@
"def convert_train(wid, index, tid, d):\n",
" \"\"\"Convert a Gotthard2 train from 12bit to 10bit.\"\"\"\n",
" gotthard2algs.convert_to_10bit(\n",
- " d[instr_mod_src][\"data.adc\"], lut, data_10bit[index, ...]\n",
+ " d[receiver][\"data.adc\"], lut, data_10bit[index, ...]\n",
" )"
]
},
@@ -293,7 +307,7 @@
" np.uint16\n",
")\n",
"empty_lut = np.stack(1280 * [np.stack([empty_lut] * 2)], axis=0)\n",
- "for mod in karabo_da:\n",
+ "for mod, receiver in zip(karabo_da, receivers):\n",
"\n",
" # Retrieve LUT constant\n",
" lut, time = get_constant_from_db_and_time(\n",
@@ -308,10 +322,7 @@
" print_once=False,\n",
" )\n",
" print(f\"Retrieved LUT constant with creation-time {time}\")\n",
- " # Path to pixels ADC values\n",
- " instr_mod_src = instrument_src.format(int(mod[-2:]))\n",
"\n",
- " # TODO: Validate the final shape to store constants.\n",
" cshape = (1280, 2, 3)\n",
"\n",
" offset_map[mod] = context.alloc(shape=cshape, dtype=np.float32)\n",
@@ -320,10 +331,10 @@
"\n",
" for run_num, [gain, run_dc] in run_dcs_dict.items():\n",
" step_timer.start()\n",
- " n_trains = specify_trains_to_process(run_dc[instr_mod_src, \"data.adc\"])\n",
+ " n_trains = specify_trains_to_process(run_dc[receiver, \"data.adc\"])\n",
"\n",
" # Select requested number of trains to process.\n",
- " dc = run_dc.select(instr_mod_src, require_all=True).select_trains(\n",
+ " dc = run_dc.select(receiver, require_all=True).select_trains(\n",
" np.s_[:n_trains]\n",
" )\n",
"\n",
@@ -332,7 +343,7 @@
" step_timer.start()\n",
" # Convert 12bit data to 10bit\n",
" data_10bit = context.alloc(\n",
- " shape=dc[instr_mod_src, \"data.adc\"].shape, dtype=np.float32\n",
+ " shape=dc[receiver, \"data.adc\"].shape, dtype=np.float32\n",
" )\n",
" context.map(convert_train, dc)\n",
" step_timer.done_step(\"convert to 10bit\")\n",
@@ -360,7 +371,7 @@
" context.map(offset_noise_cell, (even_data, odd_data))\n",
"\n",
" # Split even and odd gain data.\n",
- " data_gain = dc[instr_mod_src, \"data.gain\"].ndarray()\n",
+ " data_gain = dc[receiver, \"data.gain\"].ndarray()\n",
" even_gain = data_gain[:, 20::2, :]\n",
" odd_gain = data_gain[:, 21::2, :]\n",
" raw_g = 3 if gain == 2 else gain\n",
@@ -444,10 +455,10 @@
" ax.set_xticks(np.arange(0, 1281, 80))\n",
" ax.set_xlabel(\"Stripes #\")\n",
" ax.set_xlabel(\"BadPixels\")\n",
- " ax.set_title(f\"Cell {cell} - Module {mod} ({pdu})\")\n",
+ " ax.set_title(f\"BadPixels map - Cell {cell} - Module {mod} ({pdu})\")\n",
" ax.set_ylim([0, 5])\n",
" ax.legend()\n",
- " pass\n",
+ " plt.show()\n",
"step_timer.done_step(f\"Creating bad pixels constant and plotting it.\")"
]
},
@@ -458,8 +469,10 @@
"metadata": {},
"outputs": [],
"source": [
- "for mod, pdu in zip(karabo_da, db_modules):\n",
- " for cons, cname in zip([offset_map, noise_map], [\"Offset\", \"Noise\"]):\n",
+ "for cons, cname in zip([offset_map, noise_map], [\"Offset\", \"Noise\"]):\n",
+ " for mod, pdu in zip(karabo_da, db_modules):\n",
+ " display(Markdown(f\"### {cname} for module {mod}:\"))\n",
+ "\n",
" for cell in [0, 1]:\n",
" fig, ax = plt.subplots(figsize=(10, 5))\n",
" for g_idx in [0, 1, 2]:\n",
@@ -469,7 +482,7 @@
" ax.set_xlabel(cname)\n",
" ax.set_title(f\"{cname} map - Cell {cell} - Module {mod} ({pdu})\")\n",
" ax.legend()\n",
- " pass"
+ " plt.show()"
]
},
{