diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
index cf3651df73e977a25de5487419dcacd14feac77b..91e853812ce551bef66bb714e89ef67a8d0d9ea7 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
@@ -20,8 +20,7 @@
"ExecuteTime": {
"end_time": "2019-02-20T12:42:51.255184Z",
"start_time": "2019-02-20T12:42:51.225500Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -62,8 +61,7 @@
"ExecuteTime": {
"end_time": "2019-02-20T12:42:52.599660Z",
"start_time": "2019-02-20T12:42:51.472138Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -137,8 +135,7 @@
"ExecuteTime": {
"end_time": "2019-02-20T12:42:52.608214Z",
"start_time": "2019-02-20T12:42:52.601257Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -168,8 +165,7 @@
"ExecuteTime": {
"end_time": "2019-02-20T12:42:54.024731Z",
"start_time": "2019-02-20T12:42:53.901555Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -199,8 +195,7 @@
"ExecuteTime": {
"end_time": "2019-02-20T10:50:55.839958Z",
"start_time": "2019-02-20T10:50:55.468134Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -365,8 +360,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T09:38:18.220833Z",
"start_time": "2018-12-06T09:38:17.926616Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -386,8 +380,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T09:38:18.234582Z",
"start_time": "2018-12-06T09:38:18.222838Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -411,6 +404,16 @@
" store_file.close()"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "proposal = list(filter(None, in_folder.strip('/').split('/')))[-2]\n",
+ "file_loc = 'proposal:{} runs:{} {} {}'.format(proposal, run_low, run_med, run_high)"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -418,8 +421,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T09:49:32.449330Z",
"start_time": "2018-12-06T09:49:20.231607Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -442,6 +444,7 @@
" metadata.calibration_constant_version = Versions.Now(device=device)\n",
" else:\n",
" metadata.calibration_constant_version = Versions.Timespan(device=device, start=creation_time)\n",
+ " metadata.calibration_constant_version.raw_data_location = file_loc\n",
" metadata.send(cal_db_interface, timeout=3000000)\n",
" \n",
" \n",
@@ -459,6 +462,7 @@
" metadata.calibration_constant_version = Versions.Now(device=device)\n",
" else:\n",
" metadata.calibration_constant_version = Versions.Timespan(device=device, start=creation_time)\n",
+ " metadata.calibration_constant_version.raw_data_location = file_loc\n",
" metadata.send(cal_db_interface, timeout=3000000)\n",
" \n",
" metadata = ConstantMetaData()\n",
@@ -475,6 +479,7 @@
" metadata.calibration_constant_version = Versions.Now(device=device)\n",
" else:\n",
" metadata.calibration_constant_version = Versions.Timespan(device=device, start=creation_time)\n",
+ " metadata.calibration_constant_version.raw_data_location = file_loc\n",
" metadata.send(cal_db_interface, timeout=3000000)\n",
" \n",
" metadata = ConstantMetaData()\n",
@@ -491,6 +496,7 @@
" metadata.calibration_constant_version = Versions.Now(device=device)\n",
" else:\n",
" metadata.calibration_constant_version = Versions.Timespan(device=device, start=creation_time)\n",
+ " metadata.calibration_constant_version.raw_data_location = file_loc\n",
" metadata.send(cal_db_interface, timeout=3000000)"
]
},
@@ -518,7 +524,6 @@
"end_time": "2018-12-06T09:49:14.540552Z",
"start_time": "2018-12-06T09:49:13.009674Z"
},
- "collapsed": true,
"scrolled": false
},
"outputs": [],
@@ -540,7 +545,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "collapsed": true,
"scrolled": false
},
"outputs": [],
@@ -561,7 +565,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "collapsed": true,
"scrolled": true
},
"outputs": [],
@@ -591,7 +594,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "collapsed": true,
"scrolled": false
},
"outputs": [],
@@ -618,9 +620,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"gain = 1\n",
@@ -638,9 +638,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"gain = 2\n",
@@ -661,7 +659,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "collapsed": true,
"scrolled": false
},
"outputs": [],
@@ -674,7 +671,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "collapsed": true,
"scrolled": false
},
"outputs": [],
@@ -687,7 +683,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "collapsed": true,
"scrolled": false
},
"outputs": [],
@@ -699,9 +694,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"bad_pixel_aggregate_g = OrderedDict()\n",
@@ -728,7 +721,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.6"
+ "version": "3.6.7"
}
},
"nbformat": 4,
diff --git a/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC.ipynb b/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC.ipynb
index 2f89983fefcb7c75f8a1ddc1bafe7ae9f8b86f95..6ee85833c3b5a5bad96148f38525a4b54c138b56 100644
--- a/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC.ipynb
+++ b/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC.ipynb
@@ -20,8 +20,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T10:54:38.999974Z",
"start_time": "2018-12-06T10:54:38.983406Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -54,8 +53,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T10:54:39.190907Z",
"start_time": "2018-12-06T10:54:39.186154Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -70,8 +68,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T10:54:39.467334Z",
"start_time": "2018-12-06T10:54:39.427784Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -114,6 +111,16 @@
"sigmaNoise = sigma_noise"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "proposal = list(filter(None, in_folder.strip('/').split('/')))[-2]\n",
+ "file_loc = 'proposal:{} runs:{}'.format(proposal, run)"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -121,8 +128,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T10:54:40.058101Z",
"start_time": "2018-12-06T10:54:40.042615Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -159,8 +165,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T10:54:40.555804Z",
"start_time": "2018-12-06T10:54:40.452978Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -204,8 +209,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T10:54:41.584031Z",
"start_time": "2018-12-06T10:54:41.578462Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -223,8 +227,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T10:54:41.899511Z",
"start_time": "2018-12-06T10:54:41.864816Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -258,8 +261,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T10:55:21.238009Z",
"start_time": "2018-12-06T10:54:54.586435Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -284,8 +286,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T10:56:20.686534Z",
"start_time": "2018-12-06T10:56:11.721829Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -342,8 +343,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T10:56:22.741284Z",
"start_time": "2018-12-06T10:56:20.688393Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -377,6 +377,7 @@
" metadata.calibration_constant_version = Versions.Now(device=device)\n",
"else:\n",
" metadata.calibration_constant_version = Versions.Timespan(device=device, start=creation_time)\n",
+ "metadata.calibration_constant_version.raw_data_location = file_loc\n",
"metadata.send(cal_db_interface)\n",
"\n",
"## noise\n",
@@ -410,6 +411,7 @@
" metadata.calibration_constant_version = Versions.Now(device=device)\n",
"else:\n",
" metadata.calibration_constant_version = Versions.Timespan(device=device, start=creation_time)\n",
+ "metadata.calibration_constant_version.raw_data_location = file_loc\n",
"metadata.send(cal_db_interface)\n",
"\n"
]
@@ -417,9 +419,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"from cal_tools.enums import BadPixels\n",
@@ -444,9 +444,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"metadata = ConstantMetaData()\n",
@@ -478,15 +476,14 @@
" metadata.calibration_constant_version = Versions.Now(device=device)\n",
"else:\n",
" metadata.calibration_constant_version = Versions.Timespan(device=device, start=creation_time)\n",
+ "metadata.calibration_constant_version.raw_data_location = file_loc\n",
"metadata.send(cal_db_interface)"
]
},
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"histCalCorr = xcal.HistogramCalculator(sensorSize, bins=200, \n",
@@ -504,9 +501,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"ho,eo,co,so = histCalCorr.get()\n",
@@ -533,9 +528,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": []
}
@@ -556,7 +549,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.6"
+ "version": "3.6.7"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
diff --git a/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC_New_Common_Mode.ipynb b/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC_New_Common_Mode.ipynb
index 148c56f21929a2f6a55da192d2d9ab01a84e24e5..001a9c3ea62f7b70ff61ec702767763bb37148f9 100644
--- a/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC_New_Common_Mode.ipynb
+++ b/notebooks/FastCCD/Characterize_Darks_NewDAQ_FastCCD_NBC_New_Common_Mode.ipynb
@@ -122,6 +122,16 @@
" return min(nImages, limit)"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "proposal = list(filter(None, in_folder.strip('/').split('/')))[-2]\n",
+ "file_loc = 'proposal:{} runs:{}'.format(proposal, run)"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -950,8 +960,9 @@
" metadata.calibration_constant_version = Versions.Timespan(device=device, start=creation_time)\n",
" \n",
" if db_output:\n",
+ " metadata.calibration_constant_version.raw_data_location = file_loc\n",
" metadata.send(cal_db_interface, timeout=cal_db_timeout) \n",
- " \n",
+ "\n",
"print(\"Calibration constants (offsetMap, noiseMapCM_2nd and bad_pixels) are sent to the calibration database.\")\n",
"print(\"Creation time is: {}\".format(creation_time))"
]
diff --git a/notebooks/LPD/LPDChar_Darks_NBC.ipynb b/notebooks/LPD/LPDChar_Darks_NBC.ipynb
index 095a747d79d835a84e091cb7a5652b89a482a4a9..521c9573b46edd894a989f17b8bf26882bb4e0ad 100644
--- a/notebooks/LPD/LPDChar_Darks_NBC.ipynb
+++ b/notebooks/LPD/LPDChar_Darks_NBC.ipynb
@@ -435,6 +435,16 @@
" }"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "proposal = list(filter(None, in_folder.strip('/').split('/')))[-2]\n",
+ "file_loc = 'proposal:{} runs:{} {} {}'.format(proposal, run_low, run_med, run_high)"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -467,6 +477,8 @@
" else:\n",
" metadata.calibration_constant_version = Versions.Timespan(device=device,\n",
" start=creation_time)\n",
+ " \n",
+ " metadata.calibration_constant_version.raw_data_location = file_loc\n",
" metadata.send(cal_db_interface, timeout=cal_db_timeout)\n",
" msg = 'Const {} for module {} was injected to the calibration DB. Begin at: {}'\n",
" print(msg.format(const, qm,\n",
diff --git a/notebooks/ePix/Characterize_Darks_ePix10K_NBC.ipynb b/notebooks/ePix/Characterize_Darks_ePix10K_NBC.ipynb
index 2e0a161879c1c80b1e7b27a1be459347dfb993ee..84e92b3f25d54fe1b2c1d910acfb98722b653cbe 100644
--- a/notebooks/ePix/Characterize_Darks_ePix10K_NBC.ipynb
+++ b/notebooks/ePix/Characterize_Darks_ePix10K_NBC.ipynb
@@ -16,9 +16,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"in_folder = '/gpfs/exfel/exp/HED/201922/p002550/raw' # input folder, required\n",
@@ -46,9 +44,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"import XFELDetAna.xfelprofiler as xprof\n",
@@ -94,11 +90,12 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
+ "proposal = list(filter(None, in_folder.strip('/').split('/')))[-2]\n",
+ "file_loc = 'proposal:{} runs:{}'.format(proposal, run)\n",
+ "\n",
"x = 356 # rows of the ePix10K\n",
"y = 384 # columns of the ePix10K\n",
"\n",
@@ -118,9 +115,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"sensorSize = [x, y]\n",
@@ -160,9 +155,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"reader = ChunkReader(filename, fastccdreaderh5.readData,\n",
@@ -175,9 +168,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"noiseCal = xcal.NoiseCalculator(sensorSize, memoryCells,\n",
@@ -192,9 +183,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"for data in reader.readChunks():\n",
@@ -215,9 +204,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"#**************OFFSET MAP HISTOGRAM***********#\n",
@@ -268,7 +255,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "collapsed": false,
"scrolled": false
},
"outputs": [],
@@ -309,7 +295,7 @@
" else:\n",
" metadata.calibration_constant_version = Versions.Timespan(device=device,\n",
" start=creation_time)\n",
- " \n",
+ " metadata.calibration_constant_version.raw_data_location = file_loc\n",
" metadata.send(cal_db_interface)\n",
" print(\"Inject {} constants from {}\".format(const_name, \n",
" metadata.calibration_constant_version.begin_at))"
@@ -318,9 +304,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": []
}
@@ -341,7 +325,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.4.3"
+ "version": "3.6.7"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
diff --git a/notebooks/ePix/Characterize_Darks_ePix_NBC.ipynb b/notebooks/ePix/Characterize_Darks_ePix_NBC.ipynb
index 979315c9f670d45e0725c509808a173dbb541df7..45dc2bd9730cf0d4bcaba0c9fb8467f541d89b30 100644
--- a/notebooks/ePix/Characterize_Darks_ePix_NBC.ipynb
+++ b/notebooks/ePix/Characterize_Darks_ePix_NBC.ipynb
@@ -16,9 +16,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"in_folder = '/gpfs/exfel/exp/MID/201930/p900071/raw' # input folder, required\n",
@@ -46,9 +44,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"import XFELDetAna.xfelprofiler as xprof\n",
@@ -77,7 +73,7 @@
"import numpy as np\n",
"import h5py\n",
"import matplotlib.pyplot as plt\n",
- "% matplotlib inline\n",
+ "%matplotlib inline\n",
"\n",
"h5path = h5path.format(instance)\n",
"h5path_t = h5path_t.format(instance)\n",
@@ -93,11 +89,12 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
+ "proposal = list(filter(None, in_folder.strip('/').split('/')))[-2]\n",
+ "file_loc = 'proposal:{} runs:{}'.format(proposal, run)\n",
+ "\n",
"x = 708 # rows of the xPix100\n",
"y = 768 # columns of the xPix100\n",
"\n",
@@ -116,9 +113,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"sensorSize = [x, y]\n",
@@ -154,9 +149,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"reader = ChunkReader(filename, fastccdreaderh5.readData,\n",
@@ -169,9 +162,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"noiseCal = xcal.NoiseCalculator(sensorSize, memoryCells,\n",
@@ -186,9 +177,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"for data in reader.readChunks():\n",
@@ -208,9 +197,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"#**************OFFSET MAP HISTOGRAM***********#\n",
@@ -261,7 +248,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "collapsed": true,
"scrolled": false
},
"outputs": [],
@@ -302,19 +288,12 @@
" metadata.calibration_constant_version = Versions.Timespan(device=device,\n",
" start=creation_time)\n",
" \n",
+ " metadata.calibration_constant_version.raw_data_location = file_loc\n",
+ " \n",
" metadata.send(cal_db_interface)\n",
" print(\"Inject {} constants from {}\".format(const_name, \n",
" metadata.calibration_constant_version.begin_at))"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": []
}
],
"metadata": {
@@ -333,7 +312,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.6"
+ "version": "3.6.7"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,