Change chapter file order and fix references

_toc.yml

@@ -11,21 +11,23 @@
 - part: "2. Spectral Indices"
   chapters:
   - file: "sources/02-overview.md"
-  - file: "sources/02a-area-of-interest-definition-and-product-download.ipynb"
+  - file: "sources/02a-data-retrieval.ipynb"
+    sections:
+    - file: "sources/02a-data-retrieval-corrupted-zip-files.ipynb"
   - file: "sources/02b-ndvi.ipynb"
     sections:
-    - file: "sources/02c-corrupted-zip-file.ipynb"
-    - file: "sources/02c-multiprocessing-benchmarks.ipynb"
-    - file: "sources/02d-cloud-masks.ipynb"
-  - file: "sources/02b-timeseries.ipynb"
-  - file: "sources/02e-spectral-indices.ipynb"
+    - file: "sources/02b-ndvi-cloud-masks.ipynb"
+  - file: "sources/02c-time-series.ipynb"
+    sections:
+    - file: "sources/02c-time-series-multiprocessing-benchmarks.ipynb"
+  - file: "sources/02d-spectral-indices.ipynb"
 - part: "3. Burn Ratio Calculations"
   chapters:
   - file: "sources/03-overview.md"
-  - file: "sources/03a-area-of-interest-definition-and-product-download.ipynb"
+  - file: "sources/03a-data-retrieval.ipynb"
     sections:
-    - file: "sources/03a-forest-fire-product-downloads.ipynb"
-  - file: "sources/03c-dnbr.ipynb"
+    - file: "sources/03a-data-retrieval-estimate.ipynb"
+  - file: "sources/03b-dnbr.ipynb"
 - part: "Appendix"
   chapters:
-  - file: "sources/XX sentinel_helpers.rst"
+  - file: "sources/xx-sentinel-helpers.rst"

sources/02a-data-retrieval-corrupted-zip-files.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# ZIP-File Corruption Issues\n",
     "\n",
-    "The Copernicus Open Access Hub has a policy of moving data into a Long-Term-Archive after a certain period of time.[^lta]\n",
+    "The Copernicus Open Access Hub has a policy of [moving data into a Long-Term-Archive after a certain period of time](\"https://scihub.copernicus.eu/userguide/LongTermArchive\").\n",
     "Retrieval of files from this offline archive is a two step process:\n",
     "\n",
     "1. A request to the URL that initializes the download for online products (`https://scihub.copernicus.eu/dhus/odata/v1/Products('$UUID')/$value`) instead initializes a data retrieval request which moves the archived file from offline to online storage.\n",
@@ -18,8 +18,6 @@
     "\n",
     "This notebook contains information about a feasible process to identify corrupted zip files and manually initialize their correct retrieval, given the number of corruptions is sufficiently small.\n",
     "\n",
-    "[^lta]: Detailed information about this is provided in the [Open Access Hub User Guide](\"https://web.archive.org/web/20210117042627/https://scihub.copernicus.eu/userguide/LongTermArchive\")\n",
-    "\n",
     "## Identification Process\n",
     "\n",
     "Using unix command line tools, the following command lists all files in a target folder in ascending order by size. The size is printed in a human-readable format in the left column."

sources/02c-time-series-multiprocessing-benchmarks.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Multi-Processing Performance Benchmarks\n",
     "\n",
-    "This section contains a performance comparison of single- and multiprocess-based calculation methods used in [](02b-timeseries.ipynb).\n",
+    "This section contains a performance comparison of single- and multiprocess-based calculation methods used in [](02c-time-series.ipynb).\n",
     "\n",
     "The `%%timeit` cell magic runs the cell content multiple times and prints statistics on those multiple runs. This reduces factors such as garbage collection pauses which influence the runtime performance and can be used to verify performance assumptions."
    ]

sources/02c-time-series.ipynb

@@ -43,9 +43,9 @@
    "source": [
     "Due to an unexpected failure of the Copernicus Open Access Hub API, several of the downloaded products were unusable due to data corruption.[^data_corruption] This is considered in the processing code by excluding the corrupted files.\n",
     "\n",
-    "Additionally, even though acceptable products were restricted [](02a-area-of-interest-definition-and-product-download.ipynb) to only those with a low cloud coverage, in some products clouds might still obscure the particular area of interest inside the products. If less than 50% of the area of interest is visible inside a particular product, the product is deemed to not contain enough usable data and skipped as well.\n",
+    "Additionally, even though acceptable products were restricted in [](02a-data-retrieval.ipynb) to only those with a low cloud coverage, in some products clouds might still obscure the particular area of interest inside the products. If less than 50% of the area of interest is visible inside a particular product, the product is deemed to not contain enough usable data and skipped as well.\n",
     "\n",
-    "[^data_corruption]: See [](02c-corrupted-zip-file.ipynb) for details.\n",
+    "[^data_corruption]: See [](02a-data-retrieval-corrupted-zip-files.ipynb) for details.\n",
     "\n",
     "## Data Processing"
    ]
@@ -246,7 +246,7 @@
     "\n",
     "The average NDVI over the area is calculated using a multiprocessing pool.[^performance_comparison]\n",
     "\n",
-    "[^performance_comparison]: [02c Multithreading.ipynb](./02c Multithreading.ipynb) contains a performance benchmark to that shows that multiprocessing does not bring any real performance for this particular calculation."
+    "[^performance_comparison]: [](./02c-time-series-multiprocessing-benchmarks.ipynb) shows that multiprocessing does not offer any real performance increase for this particular calculation."
    ]
   },
   {

sources/03a-data-retrieval-estimate.ipynb

@@ -266,7 +266,7 @@
    "metadata": {},
    "source": [
     "Which is a part of approximately 91% of the products for the entire year and therefore a download duration of roughly 67 hours.\n",
-    "This number represents a fraction of the actual processing time needed due to problems with [data corruption](02c-corrupted-zip-file.ipynb) and manual verification steps."
+    "This number represents a fraction of the actual processing time needed due to [problems with data corruption](02a-data-retrieval-corrupted-zip-files.ipynb) and manual verification steps."
    ]
   },
   {

sources/03a-data-retrieval.ipynb

@@ -320,7 +320,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The files were downloaded to the following paths, which can be copied into the notebook [](02e-spectral-indices) to calculate their NBR."
+    "The files were downloaded to the following paths, which can be copied into the notebook [](02d-spectral-indices) to calculate their NBR."
    ]
   },
   {
@@ -686,7 +686,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The downloaded products can be found at the following paths, which, like previously, can be used to calculate the NBR in the product NBR using the code in [](02e-spectral-indices)."
+    "The downloaded products can be found at the following paths, which, like previously, can be used to calculate the NBR in the product NBR using the code in [](02d-spectral-indices)."
    ]
   },
   {

sources/03b-dnbr.ipynb

@@ -18,7 +18,7 @@
     "\n",
     "## Methodology\n",
     "\n",
-    "The NBR of the products downloaded in the previous notebook is calculated using the notebook [](02e-spectral-indices).\n",
+    "The NBR of the products downloaded in the previous notebook is calculated using the notebook [](02d-spectral-indices).\n",
     "These NBR values are plotted side-by-side to get a visual impression of the changes that may have occurred between two given dates.\n",
     "The ${\\Delta}$NBR is calculated and, if showing signs of burned areas, compared to data given by the responsible German ministries.\n",
     "\n",