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@e-marshall
e-marshall committed Feb 4, 2024
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71 changes: 29 additions & 42 deletions _sources/asf_local_vrt.ipynb
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Expand Up @@ -80,22 +80,22 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"id": "2eb32b85-47b7-4e1d-baeb-48af7116ce6e",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"geopandas : 0.14.3\n",
"matplotlib: 3.8.2\n",
"dask : 2024.1.1\n",
"markdown : 3.5.2\n",
"xarray : 2024.1.1\n",
"pandas : 2.2.0\n",
"dask : 2024.1.1\n",
"numpy : 1.26.3\n",
"geopandas : 0.14.3\n",
"rioxarray : 0.15.1\n",
"xarray : 2024.1.1\n",
"markdown : 3.5.2\n",
"\n"
]
}
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"id": "e98d128b-1696-4eba-a8a6-b89b08ea2764",
"metadata": {},
"source": [
"Setup string variables to access filenames + filepaths. Currently, the file structure is organized so that each scene has its own sub-directory within `asf_rtcs`. Within each sub-directory are several files - we want to extract the tif files containing RTC imagery for the VV and VH polarizations for each scene. The function `extract_tif_fnames()` takes a path to the directory containing the sub-directories for all scenes and returns a lists of filenames for VV polarization GeoTIFF files, VH polarization GeoTIFF files and the layover-shadow mask GeoTIFF files. Separately, it returns a list of filenames for the associated README files which will be used to extract metadata later on."
"### Organizing Sentinel-1 data to create VRT objects. \n",
"\n",
"Setup string variables to access filenames + filepaths. Currently, the file structure is organized so that each scene has its own sub-directory within `asf_rtcs`. Within each sub-directory are several files - we want to extract the tif files containing RTC imagery for the VV and VH polarizations for each scene.\n",
"\n",
"The function `extract_tif_fnames()` takes a path to the directory containing the sub-directories for all scenes and returns a lists of filenames for VV polarization GeoTIFF files, VH polarization GeoTIFF files and the layover-shadow mask GeoTIFF files. Separately, it returns a list of filenames for the associated README files which will be used to extract metadata later on. "
]
},
{
Expand All @@ -268,13 +272,13 @@
"metadata": {},
"source": [
"```{note}\n",
"If you're following along in your own python environment, replace the string below named `dir_path_all` to be the location of the RTC data on your local machine (or wherever they are stored)\n",
"If you're following along in your own python environment, replace the string below named `dir_path_all` with the path to the directory containing the RTC data on your local machine, then execute `extract_tif_fnames()`. \n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 56,
"id": "dff41701-8f7e-4f22-839f-47260a04419f",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -310,7 +314,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 57,
"id": "b409a588-e769-49d1-b62b-6f585dc9599f",
"metadata": {},
"outputs": [
Expand All @@ -323,7 +327,7 @@
" ['S1A_IW_20210821T000314_DVP_RTC30_G_gpuned_748F.README.md.txt'])"
]
},
"execution_count": 7,
"execution_count": 57,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -342,7 +346,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 58,
"id": "62b2361f-961e-463f-b9fa-66d094a24b55",
"metadata": {},
"outputs": [],
Expand All @@ -364,32 +368,6 @@
" fpaths_rm.append(path_readme)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "af9d00c1-3d50-4528-8fdb-11699dd1777f",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 9,
"id": "2164c9e4-2981-4752-bb2e-5c4d738c0993",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['/home/emmamarshall/Desktop/siparcs/asf_rtc_data/asf_rtcs/S1A_IW_20210821T000314_DVP_RTC30_G_gpuned_748F_(1)/S1A_IW_20210821T000314_DVP_RTC30_G_gpuned_748F_VH.tif', '/home/emmamarshall/Desktop/siparcs/asf_rtc_data/asf_rtcs/S1A_IW_20220116T120547_DVP_RTC30_G_gpuned_0D1E_(1)/S1A_IW_20220116T120547_DVP_RTC30_G_gpuned_0D1E_VH.tif', '/home/emmamarshall/Desktop/siparcs/asf_rtc_data/asf_rtcs/S1A_IW_20210708T120545_DVP_RTC30_G_gpuned_3E89_(1)/S1A_IW_20210708T120545_DVP_RTC30_G_gpuned_3E89_VH.tif', '/home/emmamarshall/Desktop/siparcs/asf_rtc_data/asf_rtcs/S1A_IW_20220422T120547_DVP_RTC30_G_gpuned_61B6_(1)/S1A_IW_20220422T120547_DVP_RTC30_G_gpuned_61B6_VH.tif', '/home/emmamarshall/Desktop/siparcs/asf_rtc_data/asf_rtcs/S1A_IW_20220427T121354_DVP_RTC30_G_gpuned_0535_(1)/S1A_IW_20220427T121354_DVP_RTC30_G_gpuned_0535_VH.tif', '/home/emmamarshall/Desktop/siparcs/asf_rtc_data/asf_rtcs/S1A_IW_20220410T120546_DVP_RTC30_G_gpuned_F306_(1)/S1A_IW_20220410T120546_DVP_RTC30_G_gpuned_F306_VH.tif', '/home/emmamarshall/Desktop/siparcs/asf_rtc_data/asf_rtcs/S1A_IW_20220521T121420_DVP_RTC30_G_gpuned_1380_(1)/S1A_IW_20220521T121420_DVP_RTC30_G_gpuned_1380_VH.tif', '/home/emmamarshall/Desktop/siparcs/asf_rtc_data/asf_rtcs/S1A_IW_20210809T000313_DVP_RTC30_G_gpuned_ED8C_(1)/S1A_IW_20210809T000313_DVP_RTC30_G_gpuned_ED8C_VH.tif', '/home/emmamarshall/Desktop/siparcs/asf_rtc_data/asf_rtcs/S1A_IW_20210926T000315_DVP_RTC30_G_gpuned_2CBE_(1)/S1A_IW_20210926T000315_DVP_RTC30_G_gpuned_2CBE_VH.tif', '/home/emmamarshall/Desktop/siparcs/asf_rtc_data/asf_rtcs/S1A_IW_20210502T121414_DVP_RTC30_G_gpuned_1424_(1)/S1A_IW_20210502T121414_DVP_RTC30_G_gpuned_1424_VH.tif']\n"
]
}
],
"source": [
"print(fpaths_vv[0:10])"
]
},
{
"cell_type": "markdown",
"id": "c9df335f-c7ca-4b0d-8051-c4882942ffbb",
Expand All @@ -404,12 +382,16 @@
"metadata": {},
"source": [
"We will be using the `gdalbuildvrt` command. You can find out more about it [here](https://manpages.ubuntu.com/manpages/bionic/man1/gdalbuildvrt.1.html). This command can make a VRT that either tiles the listed files into a large mosaic, or places them each in a separate band of the VRT. Because we are dealing with a temporal stack of images we want to use the `-separate` flag to place each file into a band of the VRT. </br>\n",
"Because we are making a VRT from a large number of files, we'll supply a text file with the full path for each file rather than include these at the end of the command line. We'll use the same lists of filepaths that we constructed above and will write them to text files that we pass to the `gdalbuildvrt` command."
"Because we are making a VRT from a large number of files, we'll supply a text file with the full path for each file rather than include these at the end of the command line. We'll use the same lists of filepaths that we constructed above and will write them to text files that we pass to the `gdalbuildvrt` command.\n",
"\n",
"```{note}\n",
"If you are following along on your machine, be sure to replace the file paths in the below cell with the location where you would like the text files to be written.\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 59,
"id": "a8e761e2-bae8-4f41-82bc-27822a269560",
"metadata": {},
"outputs": [],
Expand All @@ -433,12 +415,17 @@
"id": "78f001f9-2f4b-4f47-a69d-14c662917011",
"metadata": {},
"source": [
"Next, we will use gdal command line tools to create the VRT objects:"
"Next, we will use gdal command line tools to create the VRT objects:\n",
"\n",
"\n",
"```{note}\n",
"If you are following along on your machine, be sure to replace the file paths in the below cell with the location of the .txt files written in the step above.\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 60,
"id": "324b2b90-ef83-4828-a083-632d547b0048",
"metadata": {},
"outputs": [
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},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 61,
"id": "463e4fe1-481b-4bfa-9abe-620e9c0f0d06",
"metadata": {},
"outputs": [],
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6 changes: 3 additions & 3 deletions _sources/dataset_comparison.ipynb
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Expand Up @@ -143,7 +143,7 @@
" fig, axs = plt.subplots(ncols=2, figsize=(15,10))\n",
"\n",
" power_to_db(asf_input.vv.isel(acq_date=timestep)).plot(ax=axs[0], cmap=plt.cm.Greys_r, label = 'ASF');\n",
" power_to_db(pc_input.sel(band='vv').isel(time=timestep)).plot(ax=axs[1], cmap=plt.cm.Greys_r, label = 'PC')"
" power_to_db(pc_input.sel(band='vv').isel(time=timestep)).plot(ax=axs[1], cmap=plt.cm.Greys_r, label = 'PC');"
]
},
{
Expand All @@ -156,7 +156,7 @@
"def single_time_mean_compare(asf_input, pc_input, time):\n",
" fig, ax = plt.subplots(figsize=(8,8))\n",
" power_to_db(asf_input['vv_'].isel(acq_date=time).mean(dim=['x','y'])).plot(ax=ax)\n",
" power_to_db(pc_input.sel(band='vv').isel(time=time).mean(dim=['x','y'])).plot(ax=ax, color='red')"
" power_to_db(pc_input.sel(band='vv').isel(time=time).mean(dim=['x','y'])).plot(ax=ax, color='red');"
]
},
{
Expand Down Expand Up @@ -6113,7 +6113,7 @@
"fig, ax = plt.subplots(figsize=(12,8))\n",
"\n",
"power_to_db(asf_subset.vv.mean(dim=['x','y'])).plot(ax=ax, color='blue', linestyle='None', marker='o', markersize=5, label = 'ASF')\n",
"power_to_db(pc_subset.sel(band='vv').mean(dim=['x','y'])).plot(ax=ax, color='red', linestyle='None', marker='o', markersize=5, label='PC')"
"power_to_db(pc_subset.sel(band='vv').mean(dim=['x','y'])).plot(ax=ax, color='red', linestyle='None', marker='o', markersize=5, label='PC');"
]
},
{
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16 changes: 14 additions & 2 deletions _sources/rtc_timeseries.ipynb
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Expand Up @@ -2136,7 +2136,7 @@
"\n",
"lakes_prj.plot(ax=ax, facecolor='none', edgecolor='blue')\n",
"\n",
"fig.suptitle('ASF RTC backscatter image, 30 Apr 2022', fontsize=14)\n"
"fig.suptitle('ASF RTC backscatter image, 30 Apr 2022', fontsize=14);\n"
]
},
{
Expand Down Expand Up @@ -3264,7 +3264,7 @@
"axs[1].set_title('VH backscatter over proglacial lakes 2021-2022')\n",
"\n",
"legend_elements = [Line2D([0], [0], color = 'r', lw = 3, label = 'lake 1'),\n",
" Line2D([0], [0], color = 'b', lw = 3, label = 'lake 2')] "
" Line2D([0], [0], color = 'b', lw = 3, label = 'lake 2')] ; "
]
},
{
Expand All @@ -3289,6 +3289,18 @@
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.13"
}
},
"nbformat": 4,
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