chores: Adds tests for raster clipping (#88)

* chores: Adds tests for raster clipping Signed-off-by: nagesh bansal <[email protected]>
weecology · Sep 18, 2023 · 92d4fe3 · 92d4fe3
1 parent 14846d9
commit 92d4fe3
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Showing 12 changed files with 284 additions and 55 deletions.
diff --git a/neonwranglerpy/fetcher/fetcher.py b/neonwranglerpy/fetcher/fetcher.py
@@ -35,7 +35,7 @@ async def _request(session, url):
         return await response.json()
 
 
-async def _download(session, url, filename, sem, month, size=None):
+async def _download(session, url, filename, sem, size=None):
     """Asynchronous function to download file from url.
 
     Parameters
@@ -58,6 +58,7 @@ async def _download(session, url, filename, sem, month, size=None):
                 size = response.content_length if not size else size
                 block = size
                 copied = 0
+
                 with open(filename, mode='wb') as f:
                     async for chunk in response.content.iter_chunked(block):
                         f.write(chunk)
@@ -66,26 +67,44 @@ async def _download(session, url, filename, sem, month, size=None):
                         # update_progressbar(progress, size)
 
 
-async def _fetcher(data, rate_limit, headers, files_to_stack_path="filesToStack"):
+async def _fetcher(data,
+                   rate_limit,
+                   headers,
+                   files_to_stack_path="filesToStack",
+                   data_type="vst"):
     """Fetcher for downloading files."""
     sem = asyncio.Semaphore(rate_limit)
     data = data['data']
-    dir_name = '.'.join(
-        ['NEON', data['productCode'], data['siteCode'], data['month'], data['release']])
-    zip_dir_path = os.path.join(files_to_stack_path, f'{dir_name}')
-    if not os.path.isdir(zip_dir_path):
-        os.mkdir(zip_dir_path)
 
     d_urls = [f['url'] for f in data["files"]]
     sizes = [f['size'] for f in data["files"]]
     f_names = [f['name'] for f in data["files"]]
-    f_paths = [pjoin(zip_dir_path, name) for name in f_names]
-    month = [data['month']]
+    if data_type == "vst":
+        dir_name = '.'.join([
+            'NEON', data['productCode'], data['siteCode'], data['month'], data['release']
+        ])
+        zip_dir_path = os.path.join(files_to_stack_path, f'{dir_name}')
+        if not os.path.isdir(zip_dir_path):
+            os.mkdir(zip_dir_path)
+        f_paths = [pjoin(zip_dir_path, name) for name in f_names]
+    else:
+        f_paths = []
+        zip_dir_path = os.path.join(files_to_stack_path, data['productCode'])
+        if not os.path.isdir(zip_dir_path):
+            os.mkdir(zip_dir_path)
+        for i in range(len(d_urls)):
+            split_path = d_urls[i].split('/')
+            dir_path = '/'.join(split_path[4:len(split_path) - 1])
+            save_dir_path = pjoin(zip_dir_path, dir_path)
+            if not os.path.exists(save_dir_path):
+                os.makedirs(save_dir_path)
+            f_paths.append(os.path.join(save_dir_path, f_names[i]))
+
     zip_url = zip(d_urls, f_paths, sizes)
     async with aiohttp.ClientSession() as session:
         tasks = []
         for url, name, sz in zip_url:
-            task = asyncio.create_task(_download(session, url, name, sem, month, sz))
+            task = asyncio.create_task(_download(session, url, name, sem, sz))
             tasks.append(task)
 
         await asyncio.gather(*tasks)
@@ -94,7 +113,7 @@ async def _fetcher(data, rate_limit, headers, files_to_stack_path="filesToStack"
 async def vst_fetcher(item, rate_limit, headers, files_to_stack_path="filesToStack"):
     """Vst fetcher gets the urls for the files of vst data."""
     data = requests.get(item).json()
-    await _fetcher(data, rate_limit, headers, files_to_stack_path)
+    await _fetcher(data, rate_limit, headers, files_to_stack_path, "vst")
 
 
 def fetcher(batch, data_type, rate_limit, headers, files_to_stack_path):
@@ -103,7 +122,8 @@ def fetcher(batch, data_type, rate_limit, headers, files_to_stack_path):
         if data_type == 'vst':
             asyncio.run(vst_fetcher(batch, rate_limit, headers, files_to_stack_path))
         elif data_type == 'aop':
-            asyncio.run(_fetcher(batch, rate_limit, headers, files_to_stack_path))
+            asyncio.run(
+                _fetcher(batch, rate_limit, headers, files_to_stack_path, data_type))
 
     except Exception as e:
         print(f"Error processing URLs: {e}")

diff --git a/neonwranglerpy/lib/crop_plot_data.py b/neonwranglerpy/lib/crop_plot_data.py
@@ -9,8 +9,9 @@
 
 def list_files(path):
     """List all the files in a path of given format."""
-    mask = path + '/**/*.[th][i5]'
-    files = glob(mask, recursive=True)
+    mask_tif = path + "/**/*.tif"
+    mask_h5 = path + "/**/*.h5"
+    files = glob(mask_tif, recursive=True) + glob(mask_h5, recursive=True)
     return files
 
 
@@ -23,12 +24,11 @@ def crop_data_to_plot(plt,
                       parallelized=False,
                       savepath=""):
     """Create shapefiles out of a vegetation structure data with lat/lon coordinates."""
-    dataset_path = os.path.normpath(dataset_path)
+    dataset_path = os.path.abspath(dataset_path)
     full_files = list_files(dataset_path)
     files = [file for file in full_files if dpID in file]
     files = [file for file in files if str(target_year) in file]
 
-    # TODO: add check if files for targeted year and product is not present
     plots = plt[['plotID', 'subplotID', 'siteID', 'utmZone', 'easting', 'northing']]
 
     plots = plots.groupby(['plotID', 'subplotID', 'siteID',

diff --git a/neonwranglerpy/lib/retrieve_aop_data.py b/neonwranglerpy/lib/retrieve_aop_data.py
@@ -23,10 +23,10 @@ def retrieve_aop_data(data, year=2019, dpID=['DP3.30006.001'], savepath=""):
     """
     coords_for_tiles = data[['plotID', 'siteID', 'utmZone', 'easting', 'northing']]
     # get tiles dimensions
-    coords_for_tiles['easting'] = (coords_for_tiles[['easting']] /
-                                   1000).astype(int) * 1000
-    coords_for_tiles['northing'] = (coords_for_tiles[['northing']] /
-                                    1000).astype(int) * 1000
+    coords_for_tiles['easting'] = (coords_for_tiles[['easting']] / 1000).astype(
+        int, errors='ignore') * 1000
+    coords_for_tiles['northing'] = (coords_for_tiles[['northing']] / 1000).astype(
+        int, errors='ignore') * 1000
     # if there are more than 1 row, drop duplicates
     if coords_for_tiles.easting.shape[0] > 1:
         # drop duplicates values

diff --git a/neonwranglerpy/utilities/byTileAOP.py b/neonwranglerpy/utilities/byTileAOP.py
@@ -77,9 +77,9 @@ def by_tile_aop(dpID, site, year, easting, northing, buffer=0, savepath=None):
     if not len(month_urls):
         print(f"There is no data for site {site} and year {year}")
 
-    if isinstance(easting, (int, float)):
-        easting = [easting]
-        northing = [northing]
+    # if isinstance(easting, (int, float)):
+    #     easting = [easting]
+    #     northing = [northing]
     # convert the easting and northing for BLAN site
     if site == "BLAN":
         if isinstance(easting, (int, list)):
@@ -124,7 +124,7 @@ def by_tile_aop(dpID, site, year, easting, northing, buffer=0, savepath=None):
     tile_northing = np.floor(northing / 1000).astype(int) * 1000
 
     file_urls = get_tile_urls(month_urls, tile_easting, tile_northing)
-    print(f"Tiles Found for Remote Sensing Data: {len(file_urls)}")
+    # print(f"Tiles Found for Remote Sensing Data: {len(file_urls)}")
     if not savepath:
         savepath = os.path.normpath(os.path.join(os.getcwd(), dpID))
     else:
@@ -133,14 +133,14 @@ def by_tile_aop(dpID, site, year, easting, northing, buffer=0, savepath=None):
     if not os.path.isdir(savepath):
         os.makedirs(savepath)
 
-    files_to_stack_path = os.path.join(savepath, "filesToStack")
-    if not os.path.isdir(files_to_stack_path):
-        os.mkdir(files_to_stack_path)
+    # files_to_stack_path = os.path.join(savepath, "filesToStack")
+    # if not os.path.isdir(files_to_stack_path):
+    #     os.mkdir(files_to_stack_path)
 
-    if files_to_stack_path:
+    if savepath:
         fetcher.run_threaded_batches(file_urls,
                                      'aop',
                                      rate_limit=2,
                                      headers=None,
-                                     savepath=files_to_stack_path)
+                                     savepath=savepath)
     return savepath
diff --git a/requirements.txt b/requirements.txt
@@ -1,17 +1,18 @@
+deepforest
 flake8-docstrings
 geopandas
+h5py
+laspy
+laspy[lazrs,laszip]
+lazrs
+numpy
+opencv-python
 pandas
 pytest
 pytest-cov
+rasterio
 requests
+sphinx-press-theme
 toml
 tox
 yapf
-sphinx-press-theme
-laspy
-lazrs
-opencv-python
-numpy
-rasterio
-deepforest
-laspy[lazrs,laszip]
diff --git a/...18_ABBY_2/L3/DiscreteLidar/CanopyHeightModelGtif/NEON_D16_ABBY_DP3_559000_5070000_CHM.tif b/...18_ABBY_2/L3/DiscreteLidar/CanopyHeightModelGtif/NEON_D16_ABBY_DP3_559000_5070000_CHM.tif
diff --git a/...screteLidar/TileBoundary/kmls/NEON_D16_ABBY_DP1_559000_5070000_classified_point_cloud.kml b/...screteLidar/TileBoundary/kmls/NEON_D16_ABBY_DP1_559000_5070000_classified_point_cloud.kml
@@ -0,0 +1,179 @@
+<kml>
+ <Document>
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+  <Style id="green">
+   <LineStyle>
+   <color>ff00ff00</color>
+   <width>1</width>
+   </LineStyle>
+  </Style>
+  <Placemark>
+  <styleUrl>#yellow</styleUrl>
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diff --git a/...screteLidar/TileBoundary/shps/NEON_D16_ABBY_DP1_559000_5070000_classified_point_cloud.dbf b/...screteLidar/TileBoundary/shps/NEON_D16_ABBY_DP1_559000_5070000_classified_point_cloud.dbf
diff --git a/...screteLidar/TileBoundary/shps/NEON_D16_ABBY_DP1_559000_5070000_classified_point_cloud.prj b/...screteLidar/TileBoundary/shps/NEON_D16_ABBY_DP1_559000_5070000_classified_point_cloud.prj
@@ -0,0 +1 @@
+PROJCS["WGS 84 / UTM 10N",GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",0],PARAMETER["central_meridian",-123],PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],PARAMETER["false_northing",0],UNIT["Meter",1]]
diff --git a/...screteLidar/TileBoundary/shps/NEON_D16_ABBY_DP1_559000_5070000_classified_point_cloud.shp b/...screteLidar/TileBoundary/shps/NEON_D16_ABBY_DP1_559000_5070000_classified_point_cloud.shp
diff --git a/...screteLidar/TileBoundary/shps/NEON_D16_ABBY_DP1_559000_5070000_classified_point_cloud.shx b/...screteLidar/TileBoundary/shps/NEON_D16_ABBY_DP1_559000_5070000_classified_point_cloud.shx