Tjh/add notebooks

README.md

@@ -43,7 +43,7 @@ The test bed is established at the USACE CHL Field REsearch Facility in Duck, No
     - conda install <package>
 
       conda install -c conda-forge cartopy
-    * netCDF4, pyproj, utm, wavespectra, progressbar, opencv-python
+    * netCDF4, pyproj, utm (cf), wavespectra (cf), progressbar (cf), opencv (cf)
 
   - there's likely more, please add as you find!!  :-[]
 

genericWorkFlow.py

@@ -96,7 +96,8 @@ def Master_workFlow(inputDict):
                                      startTime=DT.datetime.strptime(time, '%Y-%m-%dT%H:%M:%SZ'),
                                      endTime=DT.datetime.strptime(time, '%Y-%m-%dT%H:%M:%SZ') + DT.timedelta(
                                      hours=inputDict['simulationDuration']), runFlag=runFlag,
-                                     generateFlag=generateFlag, readFlag=analyzeFlag, pbsFlag=pbsFlag)
+                                     generateFlag=generateFlag, readFlag=analyzeFlag, pbsFlag=pbsFlag,
+                                     hotStartFlag=hotStartFlag)
 
                 if generateFlag is True:
                     wavePacket, windPacket, wlPacket, bathyPacket, gridFname, wrr = frontBackNEW.ww3simSetup(time,

notebooks/cshore/cshore_example.ipynb

@@ -13,6 +13,8 @@
     "from prepdata import inputOutput\n",
     "from prepdata import writeRunRead as wrr\n",
     "from testbedutils import fileHandling\n",
+    "from prepdata import py2netCDF as p2nc\n",
+    "\n",
     "\n",
     "import datetime\n",
     "import matplotlib.pyplot as plt\n",
@@ -22,6 +24,7 @@
     "import plotly\n",
     "import pickle\n",
     "import yaml\n",
+    "\n",
     "%matplotlib inline"
    ]
   },
@@ -55,20 +58,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#rawWL = go.getWL()\n",
-    "#rawwave_data8m = go.getWaveSpec('8m-array')\n",
-    "rawwave_data6m = go.getWaveData('awac-6m',spec=True)\n",
-    "#rawwind = go.getWind()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#cmtb_data = getDataFRF.getDataTestBed(d1, d1+datetime.timedelta(minutes=1))\n",
-    "#bathy_data = cmtb_data.getBathyIntegratedTransect()"
+    "rawwave_data6m = go.getWaveData('awac-6m',spec=True)"
    ]
   },
   {
@@ -99,15 +89,6 @@
     "waves = prepdata.prep_CSHOREwaves(rawwave_data6m, reltime , d1)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#Bathy stuff is really slow right now. look into it"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -120,16 +101,6 @@
     "fric_fac = 0.015"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#prof_nums = go.getBathyTransectProfNum()\n",
-    "#print(prof_nums)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -155,7 +126,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "b_dict = prepdata.prep_CSHOREbathy(bathy_data, bathy_loc, profile_num, dx, waves, fric_fac)\n",
+    "b_dict = prepdata.prep_CSHOREbathy(bathy_data, bathy_loc, dx, waves, fric_fac=fric_fac, profile_num=profile_num)\n",
     "print(bathy_data)\n",
     "print(b_dict)"
    ]
@@ -201,7 +172,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "wl_data"
+    "rawWind = go.getWind()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "windTimeList = [d1 + datetime.timedelta(seconds=tt) for tt in reltime]\n",
+    "wind_data = prepdata.prep_wind(rawWind,windTimeList)"
    ]
   },
   {
@@ -217,7 +198,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cshoreio = wrr.cshoreio(pathPrefix='/Users/rdchlth9/Codes/cmtb_refactor/notetbooks/cshore/data', fNameBase=fname+'_cmtb', versionPrefix='base',\n",
+    "cshoreio = wrr.cshoreio(workingDirectory='/Users/rdchlth9/Codes/cmtb_refactor/notetbooks/cshore/data', testName=fname+'_cmtb', versionPrefix='base',\n",
     "                     startTime=d1, endTime=d2, runFlag=True,\n",
     "                     generateFlag=True, readFlag=False)"
    ]
@@ -357,7 +338,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cshoreiofull = wrr.cshoreio(pathPrefix='/Users/rdchlth9/Codes/cmtb_refactor/notetbooks/cshore/data', fNameBase=fname+'_cmtb_full', versionPrefix='base',\n",
+    "cshoreiofull = wrr.cshoreio(workingDirectory='/Users/rdchlth9/Codes/cmtb_refactor/notetbooks/cshore/data', testName=fname+'_cmtb_full', versionPrefix='base',\n",
     "                     startTime=d1, endTime=d2, timeStep=dt, runFlag=True,\n",
     "                     generateFlag=True, readFlag=False)"
    ]
@@ -413,7 +394,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resultsfull = cshoreiofull.readAllFiles()"
+    "spatialData, pointData = cshoreiofull.readAllFiles()"
    ]
   },
   {
@@ -422,16 +403,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resultsfull['params']"
+    "spatialData['params']"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -450,8 +424,8 @@
     "yy['simulationDuration'] = simduration\n",
     "yy['modelExecutable'] = '/Users/rdchlth9/Public/cshore/src-repo/cshore.exe'\n",
     "yy['workingDirectory'] = '/data'\n",
-    "yy['netCDFdir'] = '/thredds_data'\n",
-    "yy['logfileLoc'] = '/cmtb_refactor/data'\n",
+    "yy['netCDFdir'] = '/Users/rdchlth9/Codes/cmtb_refactor/thredds_data'\n",
+    "yy['logfileLoc'] = '/Users/rdchlth9/Codes/cmtb_refactor/data'\n",
     "yy['plotFlag'] = False\n",
     "yy['generateFlag'] = True\n",
     "yy['runFlag'] = True\n",
@@ -474,7 +448,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%run ../../genericWorkFlow.py test.yaml"
+    "#%run ../../genericWorkFlow.py test.yaml"
    ]
   },
   {

yaml_files/TestBedExampleInputs/CSHORE_Input_example_v2.yml

@@ -0,0 +1,17 @@
+THREDDS: CHL
+analyzeFlag: true
+bathyLoc: survey
+endTime: '2018-03-06T00:00:00Z'
+generateFlag: true
+logfileLoc: ./cmtb_refactor/data
+modelExecutable: /Users/rdchlth9/Public/cshore/src-repo/cshore.exe
+modelSettings:
+  modelName: cshore
+  version_prefix: FIXED
+netCDFdir: ./thredds_data
+plotFlag: false
+profileNumber: 960
+runFlag: true
+simulationDuration: 24.0
+startTime: '2018-03-05T00:00:00Z'
+workingDirectory: ./data

yaml_files/TestBedExampleInputs/ww3_Input_example_v2.yml

@@ -0,0 +1,17 @@
+THREDDS: CHL
+analyzeFlag: true
+bathyLoc: survey
+endTime: '2018-03-06T00:00:00Z'
+generateFlag: true
+logfileLoc: ./cmtb_refactor/data
+modelExecutable: /Users/rdchlth9/Public/cshore/src-repo/cshore.exe
+modelSettings:
+  modelName: cshore
+  version_prefix: FIXED
+netCDFdir: ./thredds_data
+plotFlag: false
+profileNumber: 960
+runFlag: true
+simulationDuration: 24.0
+startTime: '2018-03-05T00:00:00Z'
+workingDirectory: ./data