diff --git a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
index 5ffe35f6e0ab747019c131517f07d5fecf52526d..66628bcb80ba422a243f85727193b56c891733e1 100644
--- a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
+++ b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
@@ -24,7 +24,7 @@
"source": [
"\n",
"in_folder = \"/gpfs/exfel/exp/SQS/201921/p002430/raw/\" # input folder, required\n",
- "out_folder = '/gpfs/exfel/data/scratch/xcal/test/' # output folder, required\n",
+ "out_folder = '/gpfs/exfel/data/scratch/karnem/test/' # output folder, required\n",
"path_template = 'RAW-R{:04d}-PNCCD01-S{{:05d}}.h5' # the template to use to access data\n",
"path_template_seqs = \"{}/r{:04d}/*PNCCD01-S*.h5\"\n",
"run = 746 # which run to read data from, required\n",
@@ -174,8 +174,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T15:54:23.913269Z",
"start_time": "2018-12-06T15:54:23.868910Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -206,8 +205,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T15:54:24.088948Z",
"start_time": "2018-12-06T15:54:24.059925Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -400,8 +398,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T15:54:28.343869Z",
"start_time": "2018-12-06T15:54:28.271344Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -437,52 +434,43 @@
"ExecuteTime": {
"end_time": "2018-12-06T15:54:28.771629Z",
"start_time": "2018-12-06T15:54:28.346051Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
"#************************Calculators************************#\n",
"\n",
- "\n",
- "cmCorrection = xcal.CommonModeCorrection([x, y], \n",
- " commonModeBlockSize, \n",
+ "cmCorrection = xcal.CommonModeCorrection([x, y],\n",
+ " commonModeBlockSize,\n",
" commonModeAxisR,\n",
- " nCells = memoryCells, \n",
- " noiseMap = noiseMap,\n",
- " runParallel=True,\n",
- " stats=True)\n",
- "#cmCorrection.debug()\n",
- "\n",
- "patternClassifierLH = xcal.PatternClassifier([x, y//2], \n",
- " noiseMap[:,:y//2], \n",
- " split_evt_primary_threshold, \n",
+ " parallel=False, dType=np.float32, stride=1,\n",
+ " noiseMap=noiseMap.astype(np.float32), minFrac=0)\n",
+ "# cmCorrection.debug()\n",
+ "\n",
+ "patternClassifierLH = xcal.PatternClassifier([x, y//2],\n",
+ " noiseMap[:, :y//2],\n",
+ " split_evt_primary_threshold,\n",
" split_evt_secondary_threshold,\n",
" split_evt_mip_threshold,\n",
- " tagFirstSingles = 3, \n",
- " nCells=memoryCells, \n",
- " cores=cpuCores, \n",
- " allowElongated = False,\n",
- " blockSize=[x, y//2],\n",
- " runParallel=True)\n",
- "\n",
- "\n",
- "\n",
- "patternClassifierUH = xcal.PatternClassifier([x, y//2], \n",
- " noiseMap[:, y//2:], \n",
- " split_evt_primary_threshold, \n",
- " split_evt_secondary_threshold,\n",
- " split_evt_mip_threshold,\n",
- " tagFirstSingles = 4, \n",
- " nCells=memoryCells, \n",
- " cores=cpuCores, \n",
- " allowElongated = False,\n",
- " blockSize=[x, y//2],\n",
- " runParallel=True)\n",
- "\n",
- " \n",
- "\n",
- "\n"
+ " tagFirstSingles=3,\n",
+ " nCells=memoryCells,\n",
+ " cores=cpuCores,\n",
+ " allowElongated=False,\n",
+ " blockSize=[x, y//2],\n",
+ " runParallel=True)\n",
+ "\n",
+ "\n",
+ "patternClassifierUH = xcal.PatternClassifier([x, y//2],\n",
+ " noiseMap[:, y//2:],\n",
+ " split_evt_primary_threshold,\n",
+ " split_evt_secondary_threshold,\n",
+ " split_evt_mip_threshold,\n",
+ " tagFirstSingles=4,\n",
+ " nCells=memoryCells,\n",
+ " cores=cpuCores,\n",
+ " allowElongated=False,\n",
+ " blockSize=[x, y//2],\n",
+ " runParallel=True)"
]
},
{
@@ -492,8 +480,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:08:51.886343Z",
"start_time": "2018-12-06T16:08:51.842837Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -535,8 +522,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:08:52.441784Z",
"start_time": "2018-12-06T16:08:52.437284Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -553,8 +539,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:08:53.042555Z",
"start_time": "2018-12-06T16:08:53.034522Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -569,8 +554,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:08:53.551111Z",
"start_time": "2018-12-06T16:08:53.531064Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -601,8 +585,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:10:55.917179Z",
"start_time": "2018-12-06T16:09:01.603633Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -690,7 +673,8 @@
"\n",
" patternClassifierLH._noisemap = noise[:, :x//2, :]\n",
" patternClassifierUH._noisemap = noise[:, x//2:, :]\n",
- " data = cmCorrection.correct(data)\n",
+ " data = cmCorrection.correct(data.astype(np.float32),\n",
+ " cellTable=np.zeros(data.shape[2], np.int32))\n",
" ddsetcm[...] = np.moveaxis(data, 2, 0)\n",
"\n",
" dataLH = data[:, :x//2, :]\n",
@@ -734,9 +718,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"cmStats = cmCorrection.get()"
@@ -909,8 +891,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:10:56.203219Z",
"start_time": "2018-12-06T16:10:56.191509Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -1033,7 +1014,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "collapsed": true,
"scrolled": false
},
"outputs": [],
@@ -1113,9 +1093,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": []
}