Adding alert module compatible output option

component/message/en.json

@@ -41,8 +41,11 @@
         "conf_thld": {
             "label": "Confidence threshold for accepting detected changes",
             "no_conf_thld": "No value for area threshold has been provided"
+        },
+        "alert_module": {
+            "label": "Export files compatible with the Alert Module",
+            "no_conf_thld": "No value for area threshold has been provided"
         }
-
     },
     "cumsum": {
         "folder": "Select time series folder",

component/scripts/process.py

@@ -162,9 +162,11 @@ def main(args_list):
                 dst.write(out_stack, window=window)
 
 
-def run_cumsum(ts_folder, outdir, tiles, period, bstraps, area_thld, conf_thld, out):
 
-    out.add_live_msg("Preparing processing")
+def run_cumsum(ts_folder, outdir, tiles, period, bstraps, area_thld, conf_thld, out, alert_module=False):
+
+    out.add_live_msg('Preparing processing')
+
     # create output folder and file
     outdir = cp.result_dir / outdir
     outdir.mkdir(exist_ok=True, parents=True)
@@ -253,7 +255,62 @@ def run_cumsum(ts_folder, outdir, tiles, period, bstraps, area_thld, conf_thld,
     for file in outfiles:
         Path(file).unlink()
 
+    if alert_module:
+        prepare_for_alert_module(
+            result_file,
+            result_file.with_suffix('.alert_date.tif'),
+            result_file.with_suffix('.alert_mask.tif'),
+            result_file.with_suffix('.alert_aoi.shp')
+        )
 
+def prepare_for_alert_module(cusum_change_file, out_date, out_mask, out_aoi):
+
+    import rasterio as rio
+    import numpy as np
+    from shapely.geometry import box, mapping
+    import fiona
+
+    with rio.open(cusum_change_file) as src:
+        meta = src.meta
+        arr = src.read(1)
+        bounds = src.bounds
+        crs = src.crs.to_dict()
+
+    # create a datetime array that is year 1
+    year2000array = np.array((np.ones(arr.shape).ravel()).astype('int32').astype('str'), dtype='datetime64[D]')
+
+    # create a datetime array with the YEAR of change
+    yearChangeArray = np.array(np.floor(arr.ravel()).astype('int32').astype('str'), dtype='datetime64[D]')
+
+    # create an array with the doy
+    add_change_days = np.round((arr.ravel() - np.floor(arr.ravel())) * 365).astype('int32')
+
+    # create timedelta
+    timedelta_days = ((yearChangeArray - year2000array).astype('int32') - add_change_days).reshape(arr.shape)
+
+    # reset 0s to 0s
+    timedelta_days[arr == 0] = 0
+    mask = np.nan_to_num(timedelta_days/timedelta_days).astype('uint8')
+
+    meta.update(count=1, tiled=True)
+    with rio.open(out_date, 'w', **meta) as dst:
+        dst.write(timedelta_days.astype('float32'), 1)
+
+    meta.update(dtype='uint8') 
+    with rio.open(out_mask, 'w', **meta) as dst:
+        dst.write(mask, 1)
+
+    # AOI
+    # create a Polygon from the raster bounds
+    bbox = box(*bounds)
+    # create a schema with no properties
+    schema = {'geometry': 'Polygon', 'properties': {}}
+
+    # create shapefile
+    with fiona.open(out_aoi, 'w', driver='ESRI Shapefile', crs=crs, schema=schema) as c:
+        c.write({'geometry': mapping(bbox), 'properties': {}})
+
+
 def write_logs(log_file, start, end):
 
     with log_file.open("w") as f:

component/tile/cumsum_tile.py

@@ -37,6 +37,8 @@ def __init__(self):
             class_="mt-5",
         )
         self.period = cw.DateRangeSlider(label=cm.widget.period.label)
+        self.alert_module_out = v.Switch(class_ = "ml-5",label = cm.widget.alert_module.label, v_model = False)
+
 
         # stack the advance parameters in a expandpanel
         advance_params = v.ExpansionPanels(
@@ -69,6 +71,7 @@ def __init__(self):
                 advance_params,
                 v.Html(tag="h2", children=[cm.cumsum.periods]),
                 self.period,
+                self.alert_module_out
             ],
             alert=cw.CustomAlert(),
             btn=sw.Btn(cm.cumsum.btn),
@@ -91,7 +94,8 @@ def _start_process(self, widget, event, data):
         area_thld = 0
         conf_thld = self.conf_thld.v_model
         period = self.period.v_model
-
+        alert_module_out = self.alert_module_out
+
         # check the inputs
         if not self.alert.check_input(folder, cm.widget.folder.no_folder):
             return
@@ -105,7 +109,9 @@ def _start_process(self, widget, event, data):
             return
         if not self.alert.check_input(conf_thld, cm.widget.conf_thld.no_conf_thld):
             return
-
+        if not self.alert.check_input(alert_module_out, cm.widget.conf_thld.no_conf_thld): 
+            return 
+
         # run the cumsum process
         cs.run_cumsum(
             Path(folder),
@@ -116,6 +122,7 @@ def _start_process(self, widget, event, data):
             area_thld,
             conf_thld,
             self.alert,
+            self.alert_module_out
         )
 
         # display the end of computation message

no_ui.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -15,7 +15,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,17 +28,46 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "42d058678a3f4ccc92164c2c407a8ca0",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Styles()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "dda0667643ae45d7af4823204c3135c9",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "ResizeTrigger(template=\"\\n            <script>\\n                {methods: {\\n                    jupyter_resiz…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "# load the patial files\n",
     "%run 'cumsum_ui.ipynb'"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -47,9 +76,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "8a9a0ffaae164de7b78d3218b4460c70",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "CumSumTile(align_center=True, children=[Card(children=[Html(children=['Select time series folder'], tag='h2'),…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "cumsum_tile"
    ]
@@ -78,7 +122,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.8.10"
   }
  },
  "nbformat": 4,