From 120676aaf69087cebc072d3c939eada74caea822 Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Sat, 26 Jun 2021 23:22:57 +1200
Subject: [PATCH] :package: Download and refresh ATL11 Zarr data up to 20210421

Updating the ATLAS catalog to include ATL11 data up to and including 20210421, about five months of extra data over 2c755d5cd47ccdcdebd508cfcdd01e7f0c6808a1. Had to temporarily downgrade (locally, again) to fsspec=0.7.4 and intake-xarray=0.3.2 for the ATL11 intake download code in atl06_to_atl11.ipynb to work. Yes, taking a shortcut this time by pulling the official ATL11.003 data straight from NSIDC instead of wasting a week processing it ourselves. Glad that they have cycle 03 to cycle 09 in a single HDF5 file!!

Doing more preprocessing in the atl06_to_atl11.ipynb script by adding a set_xy_and_mask function which does lon/lat to x/y coordinate conversion and masking out of low quality data points. Should save some hassle in atl11_play.ipynb. Using 2 cores instead of 8 because of memory restrictions on the HPC cluster. So yeah, basically a quick refresh over d9ad9dbb621f574c637c0599b3b3ad47257d3d11.
---
 ATL11_to_download.txt           | 8310 +++++++++++++++----------------
 atl06_to_atl11.ipynb            |  109 +-
 atl06_to_atl11.py               |   54 +-
 deepicedrain/atlas_catalog.yaml |   14 +-
 nsidc-download-ATL11.py         |  368 ++
 5 files changed, 4636 insertions(+), 4219 deletions(-)
 create mode 100644 nsidc-download-ATL11.py

diff --git a/ATL11_to_download.txt b/ATL11_to_download.txt
index cc97605..3809948 100644
--- a/ATL11_to_download.txt
+++ b/ATL11_to_download.txt
@@ -1,4159 +1,4151 @@
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000110_0308_002_01.h5
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000111_0308_002_01.h5
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000112_0308_002_01.h5
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-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000211_0308_002_01.h5
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000212_0308_002_01.h5
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000310_0308_002_01.h5
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000311_0308_002_01.h5
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000312_0308_002_01.h5
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000410_0308_002_01.h5
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000411_0308_002_01.h5
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000412_0308_002_01.h5
-https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.002/2019.03.29/ATL11_000510_0308_002_01.h5
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+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_137912_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138010_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138011_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138012_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138110_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138111_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138112_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138210_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138211_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138212_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138310_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138311_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138312_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138410_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138411_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138412_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138510_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138511_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138512_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138610_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138611_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138612_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138710_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138711_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.26/ATL11_138712_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.28/ATL11_002711_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.28/ATL11_002712_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.29/ATL11_003410_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.29/ATL11_003411_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.29/ATL11_003412_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.29/ATL11_004110_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.29/ATL11_004111_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.29/ATL11_004112_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.30/ATL11_004710_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.30/ATL11_004711_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.30/ATL11_004712_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.30/ATL11_005410_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.30/ATL11_005411_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.09.30/ATL11_005412_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.02/ATL11_007810_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.02/ATL11_007811_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.02/ATL11_007812_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.03/ATL11_009510_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.03/ATL11_009511_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.03/ATL11_009512_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.03/ATL11_010110_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.03/ATL11_010410_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.03/ATL11_010411_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.03/ATL11_010412_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.10.07/ATL11_016012_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.11.25/ATL11_091510_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.12.04/ATL11_104512_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.12.08/ATL11_110612_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2019.12.30/ATL11_005510_0309_003_01.h5
+https://n5eil01u.ecs.nsidc.org/ATLAS/ATL11.003/2020.01.31/ATL11_054212_0309_003_01.h5
diff --git a/atl06_to_atl11.ipynb b/atl06_to_atl11.ipynb
index c32cd9f..1cdde6b 100644
--- a/atl06_to_atl11.ipynb
+++ b/atl06_to_atl11.ipynb
@@ -35,15 +35,15 @@
     "import xarray as xr\n",
     "import zarr\n",
     "\n",
+    "import deepicedrain\n",
+    "\n",
     "os.environ[\"HDF5_USE_FILE_LOCKING\"] = \"FALSE\""
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "lines_to_next_cell": 1
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -53,23 +53,23 @@
        "<td style=\"vertical-align: top; border: 0px solid white\">\n",
        "<h3 style=\"text-align: left;\">Client</h3>\n",
        "<ul style=\"text-align: left; list-style: none; margin: 0; padding: 0;\">\n",
-       "  <li><b>Scheduler: </b>tcp://127.0.0.1:35153</li>\n",
+       "  <li><b>Scheduler: </b>tcp://127.0.0.1:45595</li>\n",
        "  <li><b>Dashboard: </b><a href='http://127.0.0.1:8787/status' target='_blank'>http://127.0.0.1:8787/status</a></li>\n",
        "</ul>\n",
        "</td>\n",
        "<td style=\"vertical-align: top; border: 0px solid white\">\n",
        "<h3 style=\"text-align: left;\">Cluster</h3>\n",
        "<ul style=\"text-align: left; list-style:none; margin: 0; padding: 0;\">\n",
-       "  <li><b>Workers: </b>10</li>\n",
-       "  <li><b>Cores: </b>10</li>\n",
-       "  <li><b>Memory: </b>201.22 GB</li>\n",
+       "  <li><b>Workers: </b>2</li>\n",
+       "  <li><b>Cores: </b>2</li>\n",
+       "  <li><b>Memory: </b>187.40 GiB</li>\n",
        "</ul>\n",
        "</td>\n",
        "</tr>\n",
        "</table>"
       ],
       "text/plain": [
-       "<Client: 'tcp://127.0.0.1:35153' processes=10 threads=10, memory=201.22 GB>"
+       "<Client: 'tcp://127.0.0.1:45595' processes=2 threads=2, memory=187.40 GiB>"
       ]
      },
      "execution_count": 2,
@@ -78,7 +78,7 @@
     }
    ],
    "source": [
-    "client = dask.distributed.Client(n_workers=10, threads_per_worker=1)\n",
+    "client = dask.distributed.Client(n_workers=2, threads_per_worker=1)\n",
     "client"
    ]
   },
@@ -86,7 +86,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Download ATL11 from [NSIDC](https://doi.org/10.5067/ATLAS/ATL11.002) up to cycle 8"
+    "## Download ATL11 from [NSIDC](https://doi.org/10.5067/ATLAS/ATL11.003) up to cycle 9"
    ]
   },
   {
@@ -97,7 +97,7 @@
     {
      "data": {
       "text/plain": [
-       "136"
+       "131"
       ]
      },
      "execution_count": 3,
@@ -106,7 +106,8 @@
     }
    ],
    "source": [
-    "# Submit download jobs to Client\n",
+    "# Note, need to downgrade using `pip install fsspec==0.7.4 intake-xarray==0.3.2`\n",
+    "# Get list of official ATL11 files to download\n",
     "catalog = intake.open_catalog(\"deepicedrain/atlas_catalog.yaml\")\n",
     "with open(file=\"ATL11_to_download.txt\", mode=\"r\") as f:\n",
     "    urlpaths = f.readlines()\n",
@@ -135,19 +136,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {
     "lines_to_next_cell": 2
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "100%|██████████| 136/136 [1:16:59<00:00, 33.97s/it]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Check download progress here, https://stackoverflow.com/a/37901797/6611055\n",
     "responses = []\n",
@@ -310,7 +303,7 @@
     }
    ],
    "source": [
-    "max_cycles: int = max(int(f[-11:-10]) for f in glob.glob(\"ATL11.002/*.h5\"))\n",
+    "max_cycles: int = max(int(f[-11:-10]) for f in glob.glob(\"ATL11.003/*.h5\"))\n",
     "print(f\"{max_cycles} ICESat-2 cycles available\")"
    ]
   },
@@ -352,6 +345,28 @@
   {
    "cell_type": "code",
    "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "@dask.delayed\n",
+    "def set_xy_and_mask(ds):\n",
+    "    # Calculate the EPSG:3031 x/y projection coordinates\n",
+    "    ds[\"x\"], ds[\"y\"] = deepicedrain.lonlat_to_xy(\n",
+    "        longitude=ds.longitude, latitude=ds.latitude\n",
+    "    )\n",
+    "    # Set x, y, x_atc and y_atc as coords of the xarray.Dataset instead of lon/lat\n",
+    "    ds: xr.Dataset = ds.set_coords(names=[\"x\", \"y\", \"x_atc\", \"y_atc\"])\n",
+    "    ds: xr.Dataset = ds.reset_coords(names=[\"longitude\", \"latitude\"])\n",
+    "\n",
+    "    # Mask out low quality height data\n",
+    "    ds[\"h_corr\"]: xr.DataArray = ds.h_corr.where(cond=ds.fit_quality == 0)\n",
+    "\n",
+    "    return ds"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -360,7 +375,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 1387/1387 [00:06<00:00, 206.61it/s]\n"
+      "100%|██████████| 1387/1387 [00:07<00:00, 191.92it/s]\n"
      ]
     }
    ],
@@ -369,7 +384,7 @@
     "# Also consolidate all three laser pairs pt1, pt2, pt3 into one file\n",
     "atl11_dict = {}\n",
     "for rgt in tqdm.trange(1387):\n",
-    "    atl11files: list = glob.glob(f\"ATL11.002/ATL11_{rgt+1:04d}1?_????_00?_0?.h5\")\n",
+    "    atl11files: list = glob.glob(f\"ATL11.003/ATL11_{rgt+1:04d}1?_????_00?_0?.h5\")\n",
     "\n",
     "    try:\n",
     "        assert len(atl11files) == 3  # Should be 3 files for Orbital Segments 10,11,12\n",
@@ -382,10 +397,10 @@
     "\n",
     "    if atl11files:\n",
     "        pattern: dict = intake.source.utils.reverse_format(\n",
-    "            format_string=\"ATL11.002/ATL11_{referencegroundtrack:4}{orbitalsegment:2}_{cycles:4}_{version:3}_{revision:2}.h5\",\n",
+    "            format_string=\"ATL11.003/ATL11_{referencegroundtrack:4}{orbitalsegment:2}_{cycles:4}_{version:3}_{revision:2}.h5\",\n",
     "            resolved_string=sorted(atl11files)[1],  # get the '11' one, not '10' or '12'\n",
     "        )\n",
-    "        zarrfilepath: str = \"ATL11.002z123/ATL11_{referencegroundtrack}1x_{cycles}_{version}_{revision}.zarr\".format(\n",
+    "        zarrfilepath: str = \"ATL11.003z123/ATL11_{referencegroundtrack}1x_{cycles}_{version}_{revision}.zarr\".format(\n",
     "            **pattern\n",
     "        )\n",
     "        atl11_dict[zarrfilepath] = atl11files"
@@ -393,7 +408,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -405,7 +420,9 @@
     "\n",
     "# Convert variables to correct datatype\n",
     "encoding: dict = {}\n",
-    "df: pd.DataFrame = pd.read_csv(\"ATL11/ATL11_output_attrs.csv\")[[\"field\", \"datatype\"]]\n",
+    "df: pd.DataFrame = pd.read_csv(\n",
+    "    \"https://raw.githubusercontent.com/suzanne64/ATL11/master/ATL11/package_data/ATL11_output_attrs.csv\"\n",
+    ")[[\"field\", \"datatype\"]]\n",
     "df = df.set_index(\"field\")\n",
     "for var in ds.variables:\n",
     "    desired_dtype = str(df.datatype[var]).lower()\n",
@@ -419,14 +436,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 1387/1387 [00:18<00:00, 75.32it/s]\n"
+      "100%|██████████| 1387/1387 [00:42<00:00, 33.00it/s]\n"
      ]
     }
    ],
@@ -446,6 +463,16 @@
     "            ds = dask.delayed(obj=xr.combine_by_coords)(\n",
     "                datasets=[root_ds, reference_surface_ds]\n",
     "            )\n",
+    "            # Light pre-processing\n",
+    "            ds = set_xy_and_mask(ds=ds)\n",
+    "            _rgt_array = dask.delayed(obj=np.full)(\n",
+    "                shape=ds.ref_pt.shape,\n",
+    "                fill_value=atl11file.split(\"_\")[1][:4],\n",
+    "                dtype=np.int8,\n",
+    "            )\n",
+    "            ds = dask.delayed(obj=ds.assign_coords)(\n",
+    "                referencegroundtrack=(\"ref_pt\", _rgt_array)\n",
+    "            )\n",
     "            datasets.append(ds)\n",
     "\n",
     "    dataset = dask.delayed(obj=xr.concat)(objs=datasets, dim=\"ref_pt\")\n",
@@ -457,14 +484,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 1387/1387 [31:27<00:00,  1.36s/it]\n"
+      "100%|██████████| 1387/1387 [4:58:07<00:00, 12.90s/it] \n"
      ]
     }
    ],
@@ -480,7 +507,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 14,
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -488,10 +515,10 @@
     {
      "data": {
       "text/plain": [
-       "(183932, 6)"
+       "(185448, 7)"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -503,17 +530,15 @@
   },
   {
    "cell_type": "raw",
-   "metadata": {
-    "lines_to_next_cell": 2
-   },
+   "metadata": {},
    "source": [
     "# Note, this raw conversion below takes about 11 hours\n",
     "# because HDF5 files work on a single thread...\n",
-    "for atl11file in tqdm.tqdm(iterable=sorted(glob.glob(\"ATL11.002/*.h5\"))):\n",
+    "for atl11file in tqdm.tqdm(iterable=sorted(glob.glob(\"ATL11.003/*.h5\"))):\n",
     "    name = os.path.basename(p=os.path.splitext(p=atl11file)[0])\n",
     "    zarr.convenience.copy_all(\n",
     "        source=h5py.File(name=atl11file, mode=\"r\"),\n",
-    "        dest=zarr.open_group(store=f\"ATL11.002z/{name}.zarr\", mode=\"w\"),\n",
+    "        dest=zarr.open_group(store=f\"ATL11.003z/{name}.zarr\", mode=\"w\"),\n",
     "        if_exists=\"skip\",\n",
     "        without_attrs=True,\n",
     "    )"
@@ -540,7 +565,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.8.10"
   }
  },
  "nbformat": 4,
diff --git a/atl06_to_atl11.py b/atl06_to_atl11.py
index b311228..3ce5a2c 100644
--- a/atl06_to_atl11.py
+++ b/atl06_to_atl11.py
@@ -7,7 +7,7 @@
 #       extension: .py
 #       format_name: hydrogen
 #       format_version: '1.3'
-#       jupytext_version: 1.9.1
+#       jupytext_version: 1.11.3
 #   kernelspec:
 #     display_name: deepicedrain
 #     language: python
@@ -40,17 +40,20 @@
 import xarray as xr
 import zarr
 
+import deepicedrain
+
 os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
 
 # %%
-client = dask.distributed.Client(n_workers=10, threads_per_worker=1)
+client = dask.distributed.Client(n_workers=2, threads_per_worker=1)
 client
 
 # %% [markdown]
-# ## Download ATL11 from [NSIDC](https://doi.org/10.5067/ATLAS/ATL11.002) up to cycle 8
+# ## Download ATL11 from [NSIDC](https://doi.org/10.5067/ATLAS/ATL11.003) up to cycle 9
 
 # %%
-# Submit download jobs to Client
+# Note, need to downgrade using `pip install fsspec==0.7.4 intake-xarray==0.3.2`
+# Get list of official ATL11 files to download
 catalog = intake.open_catalog("deepicedrain/atlas_catalog.yaml")
 with open(file="ATL11_to_download.txt", mode="r") as f:
     urlpaths = f.readlines()
@@ -165,7 +168,7 @@
 #         - Attributes (longitude, latitude, h_corr, delta_time, etc)
 
 # %%
-max_cycles: int = max(int(f[-11:-10]) for f in glob.glob("ATL11.002/*.h5"))
+max_cycles: int = max(int(f[-11:-10]) for f in glob.glob("ATL11.003/*.h5"))
 print(f"{max_cycles} ICESat-2 cycles available")
 
 # %%
@@ -198,12 +201,29 @@ def open_ATL11(atl11file: str, group: str) -> xr.Dataset:
     return ds
 
 
+# %%
+@dask.delayed
+def set_xy_and_mask(ds):
+    # Calculate the EPSG:3031 x/y projection coordinates
+    ds["x"], ds["y"] = deepicedrain.lonlat_to_xy(
+        longitude=ds.longitude, latitude=ds.latitude
+    )
+    # Set x, y, x_atc and y_atc as coords of the xarray.Dataset instead of lon/lat
+    ds: xr.Dataset = ds.set_coords(names=["x", "y", "x_atc", "y_atc"])
+    ds: xr.Dataset = ds.reset_coords(names=["longitude", "latitude"])
+
+    # Mask out low quality height data
+    ds["h_corr"]: xr.DataArray = ds.h_corr.where(cond=ds.fit_quality == 0)
+
+    return ds
+
+
 # %%
 # Consolidate together Antarctic orbital segments 10, 11, 12 into one file
 # Also consolidate all three laser pairs pt1, pt2, pt3 into one file
 atl11_dict = {}
 for rgt in tqdm.trange(1387):
-    atl11files: list = glob.glob(f"ATL11.002/ATL11_{rgt+1:04d}1?_????_00?_0?.h5")
+    atl11files: list = glob.glob(f"ATL11.003/ATL11_{rgt+1:04d}1?_????_00?_0?.h5")
 
     try:
         assert len(atl11files) == 3  # Should be 3 files for Orbital Segments 10,11,12
@@ -216,10 +236,10 @@ def open_ATL11(atl11file: str, group: str) -> xr.Dataset:
 
     if atl11files:
         pattern: dict = intake.source.utils.reverse_format(
-            format_string="ATL11.002/ATL11_{referencegroundtrack:4}{orbitalsegment:2}_{cycles:4}_{version:3}_{revision:2}.h5",
+            format_string="ATL11.003/ATL11_{referencegroundtrack:4}{orbitalsegment:2}_{cycles:4}_{version:3}_{revision:2}.h5",
             resolved_string=sorted(atl11files)[1],  # get the '11' one, not '10' or '12'
         )
-        zarrfilepath: str = "ATL11.002z123/ATL11_{referencegroundtrack}1x_{cycles}_{version}_{revision}.zarr".format(
+        zarrfilepath: str = "ATL11.003z123/ATL11_{referencegroundtrack}1x_{cycles}_{version}_{revision}.zarr".format(
             **pattern
         )
         atl11_dict[zarrfilepath] = atl11files
@@ -234,7 +254,9 @@ def open_ATL11(atl11file: str, group: str) -> xr.Dataset:
 
 # Convert variables to correct datatype
 encoding: dict = {}
-df: pd.DataFrame = pd.read_csv("ATL11/ATL11_output_attrs.csv")[["field", "datatype"]]
+df: pd.DataFrame = pd.read_csv(
+    "https://raw.githubusercontent.com/suzanne64/ATL11/master/ATL11/package_data/ATL11_output_attrs.csv"
+)[["field", "datatype"]]
 df = df.set_index("field")
 for var in ds.variables:
     desired_dtype = str(df.datatype[var]).lower()
@@ -261,6 +283,16 @@ def open_ATL11(atl11file: str, group: str) -> xr.Dataset:
             ds = dask.delayed(obj=xr.combine_by_coords)(
                 datasets=[root_ds, reference_surface_ds]
             )
+            # Light pre-processing
+            ds = set_xy_and_mask(ds=ds)
+            _rgt_array = dask.delayed(obj=np.full)(
+                shape=ds.ref_pt.shape,
+                fill_value=atl11file.split("_")[1][:4],
+                dtype=np.int8,
+            )
+            ds = dask.delayed(obj=ds.assign_coords)(
+                referencegroundtrack=("ref_pt", _rgt_array)
+            )
             datasets.append(ds)
 
     dataset = dask.delayed(obj=xr.concat)(objs=datasets, dim="ref_pt")
@@ -286,11 +318,11 @@ def open_ATL11(atl11file: str, group: str) -> xr.Dataset:
 # %% [raw]
 # # Note, this raw conversion below takes about 11 hours
 # # because HDF5 files work on a single thread...
-# for atl11file in tqdm.tqdm(iterable=sorted(glob.glob("ATL11.002/*.h5"))):
+# for atl11file in tqdm.tqdm(iterable=sorted(glob.glob("ATL11.003/*.h5"))):
 #     name = os.path.basename(p=os.path.splitext(p=atl11file)[0])
 #     zarr.convenience.copy_all(
 #         source=h5py.File(name=atl11file, mode="r"),
-#         dest=zarr.open_group(store=f"ATL11.002z/{name}.zarr", mode="w"),
+#         dest=zarr.open_group(store=f"ATL11.003z/{name}.zarr", mode="w"),
 #         if_exists="skip",
 #         without_attrs=True,
 #     )
diff --git a/deepicedrain/atlas_catalog.yaml b/deepicedrain/atlas_catalog.yaml
index a430c83..1c401a0 100644
--- a/deepicedrain/atlas_catalog.yaml
+++ b/deepicedrain/atlas_catalog.yaml
@@ -26,9 +26,9 @@ sources:
       date:
         description: Year, month, and day of data acquisition
         type: datetime
-        default: 2020.11.11
+        default: 2021.04.21
         min: 2018.10.14
-        max: 2020.11.11  # note missing 2018.12.09, and gap from 2019.06.27 to 2019.07.25 (inclusive)
+        max: 2021.04.21  # note missing 2018.12.09, and gap from 2019.06.27 to 2019.07.25 (inclusive)
       orbitalsegment:
         description: Orbital Segment
         type: list
@@ -36,8 +36,8 @@ sources:
       version:
         description: Version number
         type: int
-        default: 3
-        allowed: [1, 2, 3]
+        default: 4
+        allowed: [1, 2, 3, 4]
       revision:
         description: Revision number
         type: int
@@ -131,7 +131,7 @@ sources:
           type: datetime
           default: 2020.03.11
           min: 2019.03.29
-          max: 2020.03.11
+          max: 2021.04.21
         referencegroundtrack:
           description: ICESat-2 Reference Ground Track number
           type: str
@@ -144,8 +144,8 @@ sources:
         version:
           description: Version number
           type: int
-          default: 2
-          allowed: [1, 2]
+          default: 3
+          allowed: [1, 2, 3]
     driver: intake_xarray.netcdf.NetCDFSource
     metadata:
       plots:
diff --git a/nsidc-download-ATL11.py b/nsidc-download-ATL11.py
new file mode 100644
index 0000000..a73725e
--- /dev/null
+++ b/nsidc-download-ATL11.py
@@ -0,0 +1,368 @@
+#!/usr/bin/env python
+# ----------------------------------------------------------------------------
+# NSIDC Data Download Script
+#
+# Copyright (c) 2021 Regents of the University of Colorado
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# Tested in Python 2.7 and Python 3.4, 3.6, 3.7
+#
+# To run the script at a Linux, macOS, or Cygwin command-line terminal:
+#   $ python nsidc-download-ATL11.py
+#
+# On Windows, open Start menu -> Run and type cmd. Then type:
+#     python nsidc-download-ATL11.py
+#
+# The script will first search Earthdata for all matching files.
+# You will then be prompted for your Earthdata username/password
+# and the script will download the matching files.
+#
+# If you wish, you may store your Earthdata username/password in a .netrc
+# file in your $HOME directory and the script will automatically attempt to
+# read this file. The .netrc file should have the following format:
+#    machine urs.earthdata.nasa.gov login myusername password mypassword
+# where 'myusername' and 'mypassword' are your Earthdata credentials.
+#
+from __future__ import print_function
+
+import base64
+import itertools
+import json
+import netrc
+import ssl
+import sys
+from getpass import getpass
+
+try:
+    from urllib.parse import urlparse
+    from urllib.request import urlopen, Request, build_opener, HTTPCookieProcessor
+    from urllib.error import HTTPError, URLError
+except ImportError:
+    from urlparse import urlparse
+    from urllib2 import (
+        urlopen,
+        Request,
+        HTTPError,
+        URLError,
+        build_opener,
+        HTTPCookieProcessor,
+    )
+
+short_name = "ATL11"
+version = "003"
+time_start = "2019-03-29T00:00:00Z"
+time_end = "2021-04-21T20:50:43Z"
+bounding_box = ""
+polygon = ""
+filename_filter = "*1?_0?0?_003_0?.h5"
+url_list = []
+
+CMR_URL = "https://cmr.earthdata.nasa.gov"
+URS_URL = "https://urs.earthdata.nasa.gov"
+CMR_PAGE_SIZE = 2000
+CMR_FILE_URL = (
+    "{0}/search/granules.json?provider=NSIDC_ECS"
+    "&sort_key[]=start_date&sort_key[]=producer_granule_id"
+    "&scroll=true&page_size={1}".format(CMR_URL, CMR_PAGE_SIZE)
+)
+
+
+def get_username():
+    username = ""
+
+    # For Python 2/3 compatibility:
+    try:
+        do_input = raw_input  # noqa
+    except NameError:
+        do_input = input
+
+    while not username:
+        try:
+            username = do_input("Earthdata username: ")
+        except KeyboardInterrupt:
+            quit()
+    return username
+
+
+def get_password():
+    password = ""
+    while not password:
+        try:
+            password = getpass("password: ")
+        except KeyboardInterrupt:
+            quit()
+    return password
+
+
+def get_credentials(url):
+    """Get user credentials from .netrc or prompt for input."""
+    credentials = None
+    errprefix = ""
+    try:
+        info = netrc.netrc()
+        username, account, password = info.authenticators(urlparse(URS_URL).hostname)
+        errprefix = "netrc error: "
+    except Exception as e:
+        if not ("No such file" in str(e)):
+            print("netrc error: {0}".format(str(e)))
+        username = None
+        password = None
+
+    while not credentials:
+        if not username:
+            username = get_username()
+            password = get_password()
+        credentials = "{0}:{1}".format(username, password)
+        credentials = base64.b64encode(credentials.encode("ascii")).decode("ascii")
+
+        if url:
+            try:
+                req = Request(url)
+                req.add_header("Authorization", "Basic {0}".format(credentials))
+                opener = build_opener(HTTPCookieProcessor())
+                opener.open(req)
+            except HTTPError:
+                print(errprefix + "Incorrect username or password")
+                errprefix = ""
+                credentials = None
+                username = None
+                password = None
+
+    return credentials
+
+
+def build_version_query_params(version):
+    desired_pad_length = 3
+    if len(version) > desired_pad_length:
+        print('Version string too long: "{0}"'.format(version))
+        quit()
+
+    version = str(int(version))  # Strip off any leading zeros
+    query_params = ""
+
+    while len(version) <= desired_pad_length:
+        padded_version = version.zfill(desired_pad_length)
+        query_params += "&version={0}".format(padded_version)
+        desired_pad_length -= 1
+    return query_params
+
+
+def filter_add_wildcards(filter):
+    if not filter.startswith("*"):
+        filter = "*" + filter
+    if not filter.endswith("*"):
+        filter = filter + "*"
+    return filter
+
+
+def build_filename_filter(filename_filter):
+    filters = filename_filter.split(",")
+    result = "&options[producer_granule_id][pattern]=true"
+    for filter in filters:
+        result += "&producer_granule_id[]=" + filter_add_wildcards(filter)
+    return result
+
+
+def build_cmr_query_url(
+    short_name,
+    version,
+    time_start,
+    time_end,
+    bounding_box=None,
+    polygon=None,
+    filename_filter=None,
+):
+    params = "&short_name={0}".format(short_name)
+    params += build_version_query_params(version)
+    params += "&temporal[]={0},{1}".format(time_start, time_end)
+    if polygon:
+        params += "&polygon={0}".format(polygon)
+    elif bounding_box:
+        params += "&bounding_box={0}".format(bounding_box)
+    if filename_filter:
+        params += build_filename_filter(filename_filter)
+    return CMR_FILE_URL + params
+
+
+def cmr_download(urls):
+    """Download files from list of urls."""
+    if not urls:
+        return
+
+    url_count = len(urls)
+    print("Downloading {0} files...".format(url_count))
+    credentials = None
+
+    for index, url in enumerate(urls, start=1):
+        if not credentials and urlparse(url).scheme == "https":
+            credentials = get_credentials(url)
+
+        filename = url.split("/")[-1]
+        print(
+            "{0}/{1}: {2}".format(
+                str(index).zfill(len(str(url_count))), url_count, filename
+            )
+        )
+
+        try:
+            # In Python 3 we could eliminate the opener and just do 2 lines:
+            # resp = requests.get(url, auth=(username, password))
+            # open(filename, 'wb').write(resp.content)
+            req = Request(url)
+            if credentials:
+                req.add_header("Authorization", "Basic {0}".format(credentials))
+            opener = build_opener(HTTPCookieProcessor())
+            data = opener.open(req).read()
+            open(filename, "wb").write(data)
+        except HTTPError as e:
+            print("HTTP error {0}, {1}".format(e.code, e.reason))
+        except URLError as e:
+            print("URL error: {0}".format(e.reason))
+        except IOError:
+            raise
+        except KeyboardInterrupt:
+            quit()
+
+
+def cmr_filter_urls(search_results):
+    """Select only the desired data files from CMR response."""
+    if "feed" not in search_results or "entry" not in search_results["feed"]:
+        return []
+
+    entries = [e["links"] for e in search_results["feed"]["entry"] if "links" in e]
+    # Flatten "entries" to a simple list of links
+    links = list(itertools.chain(*entries))
+
+    urls = []
+    unique_filenames = set()
+    for link in links:
+        if "href" not in link:
+            # Exclude links with nothing to download
+            continue
+        if "inherited" in link and link["inherited"] is True:
+            # Why are we excluding these links?
+            continue
+        if "rel" in link and "data#" not in link["rel"]:
+            # Exclude links which are not classified by CMR as "data" or "metadata"
+            continue
+
+        if "title" in link and "opendap" in link["title"].lower():
+            # Exclude OPeNDAP links--they are responsible for many duplicates
+            # This is a hack; when the metadata is updated to properly identify
+            # non-datapool links, we should be able to do this in a non-hack way
+            continue
+
+        filename = link["href"].split("/")[-1]
+        if filename in unique_filenames:
+            # Exclude links with duplicate filenames (they would overwrite)
+            continue
+        unique_filenames.add(filename)
+
+        urls.append(link["href"])
+
+    return urls
+
+
+def cmr_search(
+    short_name,
+    version,
+    time_start,
+    time_end,
+    bounding_box="",
+    polygon="",
+    filename_filter="",
+):
+    """Perform a scrolling CMR query for files matching input criteria."""
+    cmr_query_url = build_cmr_query_url(
+        short_name=short_name,
+        version=version,
+        time_start=time_start,
+        time_end=time_end,
+        bounding_box=bounding_box,
+        polygon=polygon,
+        filename_filter=filename_filter,
+    )
+    print("Querying for data:\n\t{0}\n".format(cmr_query_url))
+
+    cmr_scroll_id = None
+    ctx = ssl.create_default_context()
+    ctx.check_hostname = False
+    ctx.verify_mode = ssl.CERT_NONE
+
+    try:
+        urls = []
+        while True:
+            req = Request(cmr_query_url)
+            if cmr_scroll_id:
+                req.add_header("cmr-scroll-id", cmr_scroll_id)
+            response = urlopen(req, context=ctx)
+            if not cmr_scroll_id:
+                # Python 2 and 3 have different case for the http headers
+                headers = {k.lower(): v for k, v in dict(response.info()).items()}
+                cmr_scroll_id = headers["cmr-scroll-id"]
+                hits = int(headers["cmr-hits"])
+                if hits > 0:
+                    print("Found {0} matches.".format(hits))
+                else:
+                    print("Found no matches.")
+            search_page = response.read()
+            search_page = json.loads(search_page.decode("utf-8"))
+            url_scroll_results = cmr_filter_urls(search_page)
+            if not url_scroll_results:
+                break
+            if hits > CMR_PAGE_SIZE:
+                print(".", end="")
+                sys.stdout.flush()
+            urls += url_scroll_results
+
+        if hits > CMR_PAGE_SIZE:
+            print()
+        return urls
+    except KeyboardInterrupt:
+        quit()
+
+
+def main():
+    global short_name, version, time_start, time_end, bounding_box, polygon, filename_filter, url_list
+
+    # Supply some default search parameters, just for testing purposes.
+    # These are only used if the parameters aren't filled in up above.
+    if "short_name" in short_name:
+        short_name = "MOD10A2"
+        version = "6"
+        time_start = "2001-01-01T00:00:00Z"
+        time_end = "2019-03-07T22:09:38Z"
+        bounding_box = ""
+        polygon = "-109,37,-102,37,-102,41,-109,41,-109,37"
+        filename_filter = "A2019"
+        url_list = []
+
+    if not url_list:
+        url_list = cmr_search(
+            short_name,
+            version,
+            time_start,
+            time_end,
+            bounding_box=bounding_box,
+            polygon=polygon,
+            filename_filter=filename_filter,
+        )
+
+    # cmr_download(url_list)
+    return url_list
+
+
+if __name__ == "__main__":
+    url_list = main()
+    url_list = [
+        f'{url.replace("DP9/", "")}\n' for url in url_list if not url.endswith("xml")
+    ]
+    with open(file="ATL11_to_download.txt", mode="w") as f:
+        f.writelines(url_list)