From bef3a9bb1d15e49a20fd8056435938c233627b4b Mon Sep 17 00:00:00 2001 From: e-marshall Date: Sun, 4 Feb 2024 03:41:33 +0000 Subject: [PATCH] deploy: 72d6a642ddbb45f1bba888ef1f37cfc0de9b93c8 --- PC_RTC.html | 10 +++++----- _sources/PC_RTC.ipynb | 10 +++++----- _sources/appendix.md | 2 +- _sources/asf_inspect.ipynb | 4 ++-- _sources/asf_local_vrt.ipynb | 4 ++-- _sources/dataset_comparison.ipynb | 8 ++++---- appendix.html | 2 +- asf_inspect.html | 4 ++-- asf_local_vrt.html | 4 ++-- dataset_comparison.html | 8 ++++---- searchindex.js | 2 +- 11 files changed, 29 insertions(+), 29 deletions(-) diff --git a/PC_RTC.html b/PC_RTC.html index 81de19b..edffd8c 100644 --- a/PC_RTC.html +++ b/PC_RTC.html @@ -7359,7 +7359,7 @@

STAC items 
time_range = '2021-01-01/2022-08-01'
@@ -7416,7 +7416,7 @@ 
STAC itemsitems is an instance of the class ItemCollection, and we can explore it via the embedded html interface (is that right?)

+
You can see that items is an instance of the class ItemCollection, and we can explore it via the embedded html interface.

 

 

 
items
@@ -322253,7 +322253,7 @@ 
STAC items.assets, .links, .STAC_extensions and .properties onto the term below.
-You can query the object programmatically for the same metadata stored in the table using dictionary syntax on the properties accessor (<– is that the write word here?).

+You can query the object programmatically for the same metadata stored in the table using dictionary syntax on the properties accessor.

 

 

 
items[0]
@@ -325417,7 +325417,7 @@ 
Reading data using xarray
 
Retrieve source granule ID#

-
It will be useful to have the granule ID for the original SAR acquisition and GRD file used to generate the RTC image. The following code demonstrates retrieving the source granule ID from the STAC metadata and adding it as a variable (coorindate?) to the xarray object  containing the RTC imagery.

+
It will be useful to have the granule ID for the original SAR acquisition and GRD file used to generate the RTC image. The following code demonstrates retrieving the source granule ID from the STAC metadata and adding it as a coordinate variable to the xarray object  containing the RTC imagery.

 

 

 
stac_item = pystac.read_file('https://planetarycomputer.microsoft.com/api/stac/v1/collections/sentinel-1-rtc/items/S1A_IW_GRDH_1SDV_20210602T120544_20210602T120609_038161_0480FD_rtc')
@@ -327890,7 +327890,7 @@ 
Retrieve source granule IDVV data from the ascending passes, or other variables you may be itnerested in.

+
You can see that there are 69 time steps from the Ascending orbital pass and that all of the same dimensions and coordinates still exist, so you can subset for just the VV data from the ascending passes, or other variables you may be interested in.

 
Let’s take a look at the two polarizations side-by-side. Below, we’ll plot the VV and VH polarizations from the same date next to each other:

 

 

diff --git a/_sources/PC_RTC.ipynb b/_sources/PC_RTC.ipynb
index 5325270..d39da17 100644
--- a/_sources/PC_RTC.ipynb
+++ b/_sources/PC_RTC.ipynb
@@ -7036,7 +7036,7 @@
    "id": "4cd26316-b0cf-4ae8-a839-1cf619714e3f",
    "metadata": {},
    "source": [
-    "In the cell below we specify the time range we're intereste in as well as the geographic area of interest."
+    "In the cell below we specify the time range we're interested in as well as the geographic area of interest."
    ]
   },
   {
@@ -7142,7 +7142,7 @@
    "id": "450d2505-8797-456a-bd8a-97d7357ab785",
    "metadata": {},
    "source": [
-    "You can see that `items` is an instance of the class `ItemCollection`, and we can explore it via the embedded html interface (is that right?)"
+    "You can see that `items` is an instance of the class `ItemCollection`, and we can explore it via the embedded html interface."
    ]
   },
   {
@@ -322169,7 +322169,7 @@
    "metadata": {},
    "source": [
     "We can also explore the object metadata outside of the table. Try typing `.assets`, `.links`, `.STAC_extensions` and `.properties` onto the term below. \n",
-    "You can query the object programmatically for the same metadata stored in the table using dictionary syntax on the `properties` accessor (<-- is that the write word here?)."
+    "You can query the object programmatically for the same metadata stored in the table using dictionary syntax on the `properties` accessor."
    ]
   },
   {
@@ -325450,7 +325450,7 @@
    "source": [
     "### Retrieve source granule ID\n",
     "\n",
-    "It will be useful to have the granule ID for the original SAR acquisition and GRD file used to generate the RTC image. The following code demonstrates retrieving the source granule ID from the STAC metadata and adding it as a variable (coorindate?) to the xarray object  containing the RTC imagery."
+    "It will be useful to have the granule ID for the original SAR acquisition and GRD file used to generate the RTC image. The following code demonstrates retrieving the source granule ID from the STAC metadata and adding it as a coordinate variable to the xarray object  containing the RTC imagery."
    ]
   },
   {
@@ -328163,7 +328163,7 @@
    "id": "da726ad2-2949-46e5-be7f-cc2ff9061280",
    "metadata": {},
    "source": [
-    "You can see that there are 69 time steps from the Ascending orbital pass and that all of the same dimensions and coordinates still exist, so you can subset for just the `VV` data from the ascending passes, or other variables you may be itnerested in.\n",
+    "You can see that there are 69 time steps from the Ascending orbital pass and that all of the same dimensions and coordinates still exist, so you can subset for just the `VV` data from the ascending passes, or other variables you may be interested in.\n",
     "\n",
     "Let's take a look at the two polarizations side-by-side. Below, we'll plot the `VV` and `VH` polarizations from the same date next to each other:"
    ]
diff --git a/_sources/appendix.md b/_sources/appendix.md
index ab01e80..aa848b4 100644
--- a/_sources/appendix.md
+++ b/_sources/appendix.md
@@ -12,7 +12,7 @@ However, for this dataset, I found that the `xr.open_mfdataset()` function wasn'
 The stack I used contains multiple scenes that cover the same area of interest (multiple viewing geometries). If you wanted to select only scenes from a single viewing geometry at the expense of a denser time series, `xr.open_mfdataset()` might work a bit better (I didn't try this so cannot say for sure)
 ```
 
-Ultimately, I decided to use the approach of creating GDAL VRT objects, and reading those in with `rioxarray.open_rasterio()` to organize the data as xarray objects. This worked much better from a memory perspective but created much more work with organizing metadata and structuring the dataset in an analysis-ready format. The `xr.open_mfdataset()` function seems like a much more efficient approach if your dataset is well-aligned with its parameters (ie. a spatially uniform stack). While it did not end up being the best tool for this task, I decided to include the notebook with the `xr.open_mfdataset()` approach anyway in case it is useful to see a demonstration of this function. I learned a lot about how to structure a `preprocess` function and many other steps working on this example. 
+Ultimately, I decided to use the approach of creating GDAL VRT objects, and reading those in with `rioxarray.open_rasterio()` to organize the data as xarray objects. This worked much better from a memory perspective but created much more work with organizing metadata and structuring the dataset in an analysis-ready format. The `xr.open_mfdataset()` function seems like a much more efficient approach if your dataset is well-aligned with its parameters (ie. a spatially uniform stack). While it did not end up being the best tool for this task, I decided to include the notebook with the `xr.open_mfdataset()` approach anyway, in case it is useful to see a demonstration of this function. I learned a lot about how to structure a `preprocess` function and many other steps working on this example. 
 
 Take a look at the notebook using `xr.open_mfdataset()` to read in stacks of ASF-processed Sentinel-1 RTC imagery files [here](asf_local_mf.ipynb)
 
diff --git a/_sources/asf_inspect.ipynb b/_sources/asf_inspect.ipynb
index 8a0dff3..f6be17c 100644
--- a/_sources/asf_inspect.ipynb
+++ b/_sources/asf_inspect.ipynb
@@ -1251,7 +1251,7 @@
    "id": "05454a5d-373f-4620-aba6-cd1fe2ff0820",
    "metadata": {},
    "source": [
-    "It looks like there are areas affected by different types of distortion on different dates. For example, in the lower left quadrant, there is a region that is blue (5 - affected by layover) on 6/7/2010 but much of that area appears to be in radar shadow on 6/10. This pattern is present throughout much of the scene with portions of area that are affected by layover in one acquisition in shadow in the next acquisition. This is due to different viewing geometries on different orbital passes: one of the above scenes was likely collected during an ascending pass and one during a descending.\n",
+    "It looks like there are areas affected by different types of distortion on different dates. For example, in the lower left quadrant, there is a region that is blue (5 - affected by layover) on 6/7/2021 but much of that area appears to be in radar shadow on 6/10/2021. This pattern is present throughout much of the scene with portions of area that are affected by layover in one acquisition in shadow in the next acquisition. This is due to different viewing geometries on different orbital passes: one of the above scenes was likely collected during an ascending pass and one during a descending.\n",
     "\n",
     "Thanks to all the setup work we did in the previous notebook, we can confirm that: "
    ]
@@ -2744,7 +2744,7 @@
    "id": "68f545c1-05c9-4f1e-b82f-5712e2a2f042",
    "metadata": {},
    "source": [
-    "Interesting, it looks like the winter and spring composites are relatively similar to one another. There also appears to be a decrease in backscatter mvoing from spring to summer. "
+    "Interesting, it looks like the winter and spring composites are relatively similar to one another. There also appears to be a decrease in backscatter moving from spring to summer. "
    ]
   },
   {
diff --git a/_sources/asf_local_vrt.ipynb b/_sources/asf_local_vrt.ipynb
index fa8808d..c0aac03 100644
--- a/_sources/asf_local_vrt.ipynb
+++ b/_sources/asf_local_vrt.ipynb
@@ -165,7 +165,7 @@
    "source": [
     "### Read in vector data \n",
     "\n",
-    "We will use this vector data object later but we will read it in as a `geopandas.GeoDataFrame` object now. It is called PC aoi because the GeoJSON file was created off of the spatial extent of the SAR dat we will access from Microsoft Planetary Computer (PC), in order to have comparable datasets.\n"
+    "We will use this vector data object later but we will read it in as a `geopandas.GeoDataFrame` object now. It is called PC aoi because the GeoJSON file was created off of the spatial extent of the SAR data we will access from Microsoft Planetary Computer (PC), in order to have comparable datasets.\n"
    ]
   },
   {
@@ -2933,7 +2933,7 @@
    "id": "115fdb7b-df78-4e5e-8761-a987cfe14b2c",
    "metadata": {},
    "source": [
-    "Clip the full object by the same AOI as above. Just as in the last notebook, we will use the [`rioxarray.clip()` method](https://corteva.github.io/rioxarray/stable/examples/clip_geom.html)."
+    "Clip the full object by the same AOI as above. We will use the [`rioxarray.clip()` method](https://corteva.github.io/rioxarray/stable/examples/clip_geom.html)."
    ]
   },
   {
diff --git a/_sources/dataset_comparison.ipynb b/_sources/dataset_comparison.ipynb
index 3d77e57..bc44c66 100644
--- a/_sources/dataset_comparison.ipynb
+++ b/_sources/dataset_comparison.ipynb
@@ -168,7 +168,7 @@
     "\n",
     "We can use the `storemagic` command `%store` to retrieve the variable we constructed and saved in a previous notebook, rather than having to create it again. Read more about this [here](https://levelup.gitconnected.com/how-to-store-variables-in-jupyter-notebook-fea8aa60a9b)\n",
     "\n",
-    "This let's use call the ASF dataset (`vrt_new`) and PC dataset (`da_pc`)"
+    "This let's us call the ASF dataset (`vrt_new`) and PC dataset (`da_pc`)"
    ]
   },
   {
@@ -2090,7 +2090,7 @@
    "source": [
     "## Extract common data take ID from granule IDs\n",
     "\n",
-    "We want to ensure that we are performing a direct comparison of the ASF and PC datasets. To do this, we would like to use the acquisition ID that is stored in the source granule name (published by ESA). In the setup notebooks we attached the entire granule IDs of the SLC images to the ASF dataset and the GRD images to the PC dataset. In the ASF data inspection notebook, we attached data take id as a non-dimensional coordianet. Now we will do the same for the Planetary Computer dataset, extracting just the 6-digit acquisition ID from the granule ID and using this for a scene-by-scene comparison."
+    "We want to ensure that we are performing a direct comparison of the ASF and PC datasets. To do this, we would like to use the acquisition ID that is stored in the source granule name (published by ESA). In the setup notebooks we attached the entire granule IDs of the SLC images to the ASF dataset and the GRD images to the PC dataset. In the ASF data inspection notebook, we attached data take id as a non-dimensional coordinate. Now we will do the same for the Planetary Computer dataset, extracting just the 6-digit acquisition ID from the granule ID and using this for a scene-by-scene comparison."
    ]
   },
   {
@@ -4026,7 +4026,7 @@
    "id": "2b49d742-a17a-4665-8387-a86a83bfef4d",
    "metadata": {},
    "source": [
-    "Now we have data take ID coordinates for both datasets. We want to find the common data take IDs between the two datasets. TO do this, I extract a list of the acquisition IDs (`data_take_id`) for both datasets and then find the intersection of the two lists (the list object `common_data_takes`)"
+    "Now we have data take ID coordinates for both datasets. We want to find the common data take IDs between the two datasets. To do this, I extract a list of the acquisition IDs (`data_take_id`) for both datasets and then find the intersection of the two lists (the list object `common_data_takes`)"
    ]
   },
   {
@@ -4067,7 +4067,7 @@
    "id": "4ca6f9fe-5ccb-4b8e-b3b9-c16012fcbcfc",
    "metadata": {},
    "source": [
-    "It looks like there are 84 RTC images that are generated from common acquisitions between the two datasets"
+    "It looks like there are 83 RTC images that are generated from common acquisitions between the two datasets"
    ]
   },
   {
diff --git a/appendix.html b/appendix.html
index f3e0917..92bb8d7 100644
--- a/appendix.html
+++ b/appendix.html
@@ -382,7 +382,7 @@ 
xr.open_mfdatas
 
Note

 
The stack I used contains multiple scenes that cover the same area of interest (multiple viewing geometries). If you wanted to select only scenes from a single viewing geometry at the expense of a denser time series, xr.open_mfdataset() might work a bit better (I didn’t try this so cannot say for sure)

 

-
Ultimately, I decided to use the approach of creating GDAL VRT objects, and reading those in with rioxarray.open_rasterio() to organize the data as xarray objects. This worked much better from a memory perspective but created much more work with organizing metadata and structuring the dataset in an analysis-ready format. The xr.open_mfdataset() function seems like a much more efficient approach if your dataset is well-aligned with its parameters (ie. a spatially uniform stack). While it did not end up being the best tool for this task, I decided to include the notebook with the xr.open_mfdataset() approach anyway in case it is useful to see a demonstration of this function. I learned a lot about how to structure a preprocess function and many other steps working on this example.

+
Ultimately, I decided to use the approach of creating GDAL VRT objects, and reading those in with rioxarray.open_rasterio() to organize the data as xarray objects. This worked much better from a memory perspective but created much more work with organizing metadata and structuring the dataset in an analysis-ready format. The xr.open_mfdataset() function seems like a much more efficient approach if your dataset is well-aligned with its parameters (ie. a spatially uniform stack). While it did not end up being the best tool for this task, I decided to include the notebook with the xr.open_mfdataset() approach anyway, in case it is useful to see a demonstration of this function. I learned a lot about how to structure a preprocess function and many other steps working on this example.

 
Take a look at the notebook using xr.open_mfdataset() to read in stacks of ASF-processed Sentinel-1 RTC imagery files here

 
In addition to the documentation linked above, some other useful resources for xr.open_mfdataset() that I found are:

 
    
diff --git a/asf_inspect.html b/asf_inspect.html
index 733ee0f..540ef38 100644
--- a/asf_inspect.html
+++ b/asf_inspect.html
@@ -1521,7 +1521,7 @@ 
    Quick visualization
 

 

-
It looks like there are areas affected by different types of distortion on different dates. For example, in the lower left quadrant, there is a region that is blue (5 - affected by layover) on 6/7/2010 but much of that area appears to be in radar shadow on 6/10. This pattern is present throughout much of the scene with portions of area that are affected by layover in one acquisition in shadow in the next acquisition. This is due to different viewing geometries on different orbital passes: one of the above scenes was likely collected during an ascending pass and one during a descending.

+
It looks like there are areas affected by different types of distortion on different dates. For example, in the lower left quadrant, there is a region that is blue (5 - affected by layover) on 6/7/2021 but much of that area appears to be in radar shadow on 6/10/2021. This pattern is present throughout much of the scene with portions of area that are affected by layover in one acquisition in shadow in the next acquisition. This is due to different viewing geometries on different orbital passes: one of the above scenes was likely collected during an ascending pass and one during a descending.

 
Thanks to all the setup work we did in the previous notebook, we can confirm that:

 

 

@@ -2885,7 +2885,7 @@ 
Looking at backscatter variability
 

 

-
Interesting, it looks like the winter and spring composites are relatively similar to one another. There also appears to be a decrease in backscatter mvoing from spring to summer.

+
Interesting, it looks like the winter and spring composites are relatively similar to one another. There also appears to be a decrease in backscatter moving from spring to summer.

 
 

 
Handling duplicate time steps#

diff --git a/asf_local_vrt.html b/asf_local_vrt.html
index 44dca1e..b4f1fac 100644
--- a/asf_local_vrt.html
+++ b/asf_local_vrt.html
@@ -556,7 +556,7 @@ 
Utility Functions
 
Read in vector data#

-
We will use this vector data object later but we will read it in as a geopandas.GeoDataFrame object now. It is called PC aoi because the GeoJSON file was created off of the spatial extent of the SAR dat we will access from Microsoft Planetary Computer (PC), in order to have comparable datasets.

+
We will use this vector data object later but we will read it in as a geopandas.GeoDataFrame object now. It is called PC aoi because the GeoJSON file was created off of the spatial extent of the SAR data we will access from Microsoft Planetary Computer (PC), in order to have comparable datasets.

 

 

 
pc_aoi = gpd.read_file('https://github.com/e-marshall/sentinel1_rtc/raw/main/hma_rtc_aoi.geojson')
@@ -3035,7 +3035,7 @@ 
Taking a look at chunking
 
Clip by vector data#

-
Clip the full object by the same AOI as above. Just as in the last notebook, we will use the rioxarray.clip() method.

+
Clip the full object by the same AOI as above. We will use the rioxarray.clip() method.

 

 

 
vrt_clip = vrt_merge.rio.clip(pc_aoi.geometry, pc_aoi.crs)
diff --git a/dataset_comparison.html b/dataset_comparison.html
index ea535b4..5af19d9 100644
--- a/dataset_comparison.html
+++ b/dataset_comparison.html
@@ -516,7 +516,7 @@ 
Utility functions
 
Read in prepared data#

 
We can use the storemagic command %store to retrieve the variable we constructed and saved in a previous notebook, rather than having to create it again. Read more about this here

-
This let’s use call the ASF dataset (vrt_new) and PC dataset (da_pc)

+
This let’s us call the ASF dataset (vrt_new) and PC dataset (da_pc)

 

 

 
%store -r vrt_new da_pc
@@ -2342,7 +2342,7 @@ 
Read in prepared data
 

 
Extract common data take ID from granule IDs#

-
We want to ensure that we are performing a direct comparison of the ASF and PC datasets. To do this, we would like to use the acquisition ID that is stored in the source granule name (published by ESA). In the setup notebooks we attached the entire granule IDs of the SLC images to the ASF dataset and the GRD images to the PC dataset. In the ASF data inspection notebook, we attached data take id as a non-dimensional coordianet. Now we will do the same for the Planetary Computer dataset, extracting just the 6-digit acquisition ID from the granule ID and using this for a scene-by-scene comparison.

+
We want to ensure that we are performing a direct comparison of the ASF and PC datasets. To do this, we would like to use the acquisition ID that is stored in the source granule name (published by ESA). In the setup notebooks we attached the entire granule IDs of the SLC images to the ASF dataset and the GRD images to the PC dataset. In the ASF data inspection notebook, we attached data take id as a non-dimensional coordinate. Now we will do the same for the Planetary Computer dataset, extracting just the 6-digit acquisition ID from the granule ID and using this for a scene-by-scene comparison.

 

 

 
data_take_pc = [str(da_pc.isel(time=t).granule_id.values)[56:] for t in range(len(da_pc.time))]
@@ -4181,7 +4181,7 @@ 
Extract common data take ID from granule IDs
 
Subset to only common data takes#

-
Now we have data take ID coordinates for both datasets. We want to find the common data take IDs between the two datasets. TO do this, I extract a list of the acquisition IDs (data_take_id) for both datasets and then find the intersection of the two lists (the list object common_data_takes)

+
Now we have data take ID coordinates for both datasets. We want to find the common data take IDs between the two datasets. To do this, I extract a list of the acquisition IDs (data_take_id) for both datasets and then find the intersection of the two lists (the list object common_data_takes)

 

 

 
pc_data_take_ls = list(da_pc.data_take_id.values)
@@ -4203,7 +4203,7 @@ 
Subset to only common data takes.isin() method is very useful for this type of selection.

 

 

diff --git a/searchindex.js b/searchindex.js
index 885339f..22f3244 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["Acknowledgments", "PC_RTC", "References", "Summary", "appendix", "asf_inspect", "asf_local_mf", "asf_local_vrt", "ch1_root", "ch2_root", "dataset_comparison", "intro", "rtc_timeseries", "software"], "filenames": ["Acknowledgments.md", "PC_RTC.ipynb", "References.md", "Summary.md", "appendix.md", "asf_inspect.ipynb", "asf_local_mf.ipynb", "asf_local_vrt.ipynb", "ch1_root.md", "ch2_root.md", "dataset_comparison.ipynb", "intro.md", "rtc_timeseries.ipynb", "software.ipynb"], "titles": ["Acknowledgments", "Microsoft Planetary Computer Sentinel-1 RTC Imagery", "References", "Summary", "Appendix", "ASF-processed RTC data inspection", "Xarray open_mfdataset() approach", "GDAL VRT approach", "Data cleaning and organization", "Dataset comparison and preliminary analysis", "RTC dataset comparison", "Introduction", "Applied example: RTC time series analysis", "Software + Data"], "terms": {"thi": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13], "tutori": [0, 1, 3, 5, 6, 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