created merge prototype

AUVAbyssWorkflow_merge-multiplesurveys.ipynb

@@ -99,12 +99,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {
-    "collapsed": true,
     "scrolled": true
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[Errno 2] No such file or directory: '/enter/path/here'\n",
+      "/home/jochen/workspace/MBSystemWorkflow/AUVAbyssWorkflow\n"
+     ]
+    }
+   ],
    "source": [
     "rootpath=\"/enter/path/here\"\n",
     "%cd $rootpath\n",
@@ -113,7 +121,9 @@
     "navadjustProjectName = \"targetarea\"\n",
     "\n",
     "# datalists\n",
-    "datalist_navadjust = navadjustProjectName + \".mb-1\""
+    "datalist_navadjust = navadjustProjectName + \".mb-1\"\n",
+    "\n",
+    "file_ending = \".mb88\""
    ]
   },
   {
@@ -190,6 +200,103 @@
     "\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Merge Prototype"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(navadjustProjectName)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#define merge variables\n",
+    "mission_a = \"0000\"\n",
+    "mission_b = \"0001\"\n",
+    "processing_level = \"pppp\" #after processing navadjusted files\n",
+    "\n",
+    "datalistmerged = \"datalistmerged_\" + mission_a + \"-\" + mission_b + \"_\" + processing_level + \".mb-1\"\n",
+    "\n",
+    "plotname = navadjustProjectName + \"_\" + mission_a + \"-\" + mission_b + \"_merge-nav\"\n",
+    "gridname = navadjustProjectName + \"_\" + mission_a + \"-\" + mission_b + \"_merge_3m\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%cd $rootpath\n",
+    "!mbnavadjust"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%cd $rootpath\n",
+    "# process data using datalist automatically created by mbnavadjust\n",
+    "!mbprocess -I$datalist_navadjust -V"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%cd $rootpath\n",
+    "# generate new datalist of processed files\n",
+    "searchString = \"*\" + processing_level + file_ending\n",
+    "!ls -1 $searchString > $datalistmerged"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%cd $rootpath\n",
+    "# Plot navigation\n",
+    "!mbm_plot -I$datalistmerged -N -O$plotname\n",
+    "execName = plotnames + \".cmd\"\n",
+    "!./$execName"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%cd $rootpath\n",
+    "# Creating arcAscii grid of merged surveys\n",
+    "!mbgrid -I$datalistmerged -A2 -G4 -E3/0.0! -O$gridname"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Example"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -760,21 +867,21 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 2",
    "language": "python",
-   "name": "python3"
+   "name": "python2"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 3
+    "version": 2
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.6.1"
+   "pygments_lexer": "ipython2",
+   "version": "2.7.12"
   }
  },
  "nbformat": 4,