Merge pull request #32 from eEcoLiDAR/development

Development
eEcoLiDAR · May 25, 2020 · 556a1f2 · 556a1f2
2 parents 53f0ce1 + bc6c944
commit 556a1f2
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diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # Laserfarm
 
-[![Actions Status](https://github.com/eEcoLiDAR/Laserfarm/workflows/build%20and%20test/badge.svg?branch=development)](https://github.com/eEcoLiDAR/Laserfarm/actions)
-[![codecov](https://codecov.io/gh/eEcoLiDAR/Laserfarm/branch/development/graph/badge.svg)](http://codecov.io/github/eEcoLiDAR/Laserfarm/branch/development)
+[![Actions Status](https://github.com/eEcoLiDAR/Laserfarm/workflows/build%20and%20test/badge.svg)](https://github.com/eEcoLiDAR/Laserfarm/actions)
+[![codecov](https://codecov.io/gh/eEcoLiDAR/Laserfarm/branch/master/graph/badge.svg)](https://codecov.io/gh/eEcoLiDAR/Laserfarm)
 [![Documentation Status](https://readthedocs.org/projects/Laserfarm/badge/?version=latest)](https://laserfarm.readthedocs.io/en/latest/?badge=latest)
 
 Laserfarm (Laserchicken Framework for Applications in Research in Macro-ecology) provides a FOSS wrapper to 

diff --git a/docs/user_manual.rst b/docs/user_manual.rst
@@ -443,7 +443,7 @@ Finally, Python scripts and pipeline configuration files that have been used to
 local machines or on a virtual `docker-container-based cluster`_ can be found `here`_.
 
 .. _docker-container-based cluster: https://github.com/eEcoLiDAR/dockerTestCluster
-.. _here: https://github.com/eEcoLiDAR/Laserfarm/tree/development/examples
+.. _here: https://github.com/eEcoLiDAR/Laserfarm/tree/master/examples
 
 Current Limitations
 -------------------

diff --git a/workflow.ipynb b/workflow.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,19 +41,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WebDAV username: fnattin4\n",
-      "WebDAV password: ········\n",
-      "Date last run (YYYY-MM-DD): 2020-01-01\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "webdav_login = input('WebDAV username: ')\n",
     "webdav_password = getpass.getpass('WebDAV password: ')\n",
@@ -69,7 +59,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -93,27 +83,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div style='background-color: #f2f2f2; display: inline-block; padding: 10px; border: 1px solid #999999;'>\n",
-       "  <h3>LocalCluster</h3>\n",
-       "  <ul>\n",
-       "    <li><b>Dashboard: </b><a href='http://127.0.0.1:8787/status' target='_blank'>http://127.0.0.1:8787/status</a>\n",
-       "  </ul>\n",
-       "</div>\n"
-      ],
-      "text/plain": [
-       "LocalCluster('tcp://127.0.0.1:55601', workers=2, threads=2, memory=17.18 GB)"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "local_tmp = pathlib.Path('/tmp')\n",
     "cluster = LocalCluster(processes=True, \n",
@@ -145,17 +117,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Retrieve and retile: 3 LAZ files\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# dCache path to raw LAZ files \n",
     "remote_path_ahn = remote_path_root / 'test_pipeline/test_full/raw'\n",
@@ -180,7 +144,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -202,7 +166,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -233,17 +197,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Retrieve and process: 4 tiles\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# target mesh size & list of features\n",
     "tile_mesh_size = 10.\n",
@@ -261,7 +217,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -271,11 +227,11 @@
     "    'pullremote': remote_path_retiled.as_posix(),\n",
     "    'load': {'attributes': ['raw_classification']},\n",
     "    'normalize': 1,\n",
-    "#     'apply_filter': {\n",
-    "#         'filter_type': 'select_equal', \n",
-    "#         'attribute': 'raw_classification',\n",
-    "#         'value': #ground surface (2), water (9), buildings (6), artificial objects (26), vegetation (?), and unclassified (1)\n",
-    "#     },\n",
+    "    'apply_filter': {\n",
+    "        'filter_type': 'select_equal', \n",
+    "        'attribute': 'raw_classification',\n",
+    "        'value': [1, 6]#ground surface (2), water (9), buildings (6), artificial objects (26), vegetation (?), and unclassified (1)\n",
+    "    },\n",
     "    'generate_targets': {\n",
     "        'tile_mesh_size' : tile_mesh_size,\n",
     "        'validate' : True,\n",
@@ -291,7 +247,7 @@
     "        'multi_band_files': False\n",
     "    },\n",
     "    'pushremote': remote_path_targets.as_posix(),\n",
-    "    'cleanlocalfs': {}\n",
+    "#     'cleanlocalfs': {}\n",
     "}\n",
     "\n",
     "# write input dictionary to JSON file\n",
@@ -301,7 +257,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -333,7 +289,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -343,7 +299,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -365,7 +321,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -395,28 +351,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "distributed.client - ERROR - Failed to reconnect to scheduler after 10.00 seconds, closing client\n",
-      "distributed.client - ERROR - Failed to reconnect to scheduler after 10.00 seconds, closing client\n",
-      "distributed.client - ERROR - Failed to reconnect to scheduler after 10.00 seconds, closing client\n",
-      "_GatheringFuture exception was never retrieved\n",
-      "future: <_GatheringFuture finished exception=CancelledError()>\n",
-      "asyncio.exceptions.CancelledError\n",
-      "_GatheringFuture exception was never retrieved\n",
-      "future: <_GatheringFuture finished exception=CancelledError()>\n",
-      "asyncio.exceptions.CancelledError\n",
-      "_GatheringFuture exception was never retrieved\n",
-      "future: <_GatheringFuture finished exception=CancelledError()>\n",
-      "asyncio.exceptions.CancelledError\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "cluster.close()"
    ]