Reverting my changes

Author: Chris-Schnaufer

vignettes/03-get-images-python.Rmd

@@ -1,100 +1 @@
----
-title: "Get Source Image Files"
-output: html_document
----
-
-# Objective: To be able to demonstrate how to locate and retrieve RGB image files
-
-This vignette shows how to locate and retrieve image files associated with growing Season 6 
-from the University of Arizona's [Maricopa Agricultural Center](http://cals-mac.arizona.edu/) 
-using Python. The files are stored online on the data management system Clowder, 
-which is accessed using an API. We will be working with the image files generated during the 
-month of May by limiting the requests to that time period.
-
-After completing this vignette it should be possible to search for and retrieve other
-files through the use of the API.
-
-As an added bonus we've also included an exmple of how to retrieve the list of available 
-sensor names through the API. By using the sensor names returned, it's possible to retrieve
-other files containing the data the sensors have collected.
-
-## Locating the images
-
-To begin looking for files, a sensor name and site name are needed. We will be using 
-'RGB GeoTIFFs Datasets' as the sensor name and '' as the site name. Later in this
-vignette we show how to retrieve the list of available sensors.
-
-As mentioned in the overview, the url string will point to the API to use. In this case
-we'll be using "https://terraref.ncsa.illinois.edu/clowder/api" and the key will be the
-one you received in an email.
-
-```{python eval=FALSE}
-from terrautils.products import get_file_listing
-
-url = 'https://terraref.ncsa.illinois.edu/clowder/api'
-key = 'YOUR_KEY_GOES_HERE'
-sensor = 'RGB GeoTIFFs Datasets'
-sitename = ''
-files = get_file_listing(None, url, key, sensor, sitename,
-                   since='2018-05-01', until='2018-05-31')
-```
-
-The `files` variable now contains an array of all the file in the datasets that match the
-sensor in the plot for the month of May. When performing you own queries it's possible that there
-are no matches found and the `files` array would be empty.
-
-# Retrieving the images
-
-Now that we have a list of files we can retrieve them one-by-one. We do this by creating a URL
-that identifies the file to retrieve, making the API call to retrieve the file contents, and writing
-the contents to disk.
-
-To create the correct URL we start with the one defined before and attach the keyword '/files/'
-followed by the ID of each file. Assuming we have a file ID of '111', the final URL for retrieving 
-the file would be: 
-
-``` {sh eval=FALSE}
-https://terraref.ncsa.illinois.edu/clowder/api/files/111
-```
-
-By looping through each of the returned files from the previous example, and using their ID and 
-filename, we can retrieve the files from the server and store them locally. 
-
-We are streaming the data returned from our server request (`stream=True` in the code below) due to 
-the high probability of large file sizes. If the `stream=True` parameter was omitted the file's entire 
-contents would be in the `r` variable which could then be written to the local file.
-
-```{python eval=FALSE}
-# We are using the same `url` and `key` variables declared in the previous example above.
-filesurl = url + '/files/'
-params={ 'key': key }
-
-for f in files:
-  r = requests.get(fileurl +  f.id, params=params, stream=True)
-  with open(f.filename, 'wb') as o:
-        for chunk in r.iter_content(chunk_size=1024): 
-            if chunk:
-                o.write(chunk)
-     
-```
-
-The images are now stored on the local file system.
-
-# Retrieving sensor names
-
-In this section we retrieve the names of different sensor types that are available. This will
-allow you to retrieve files other than those containing RBG image data.
-
-```{python eval=FALSE}
-# We are using the same `url` and `key` variables declared in the previous example above.
-from terrautils.products import get_sensor_list, unique_sensor_names
-
-sensors = get_sensor_list(None, url, key)
-names = unique_sensor_names(sensors)
-```
-
-The variable `names` will now contain the list of all available sensors. Using these sensor
-names it's possible to use the above search to locate and then retrieve additional data files.
-Substitute the new sensor name for 'RGB GeoTIFFs Datasets' where the variable `sensor` is 
-assigned above.
-
+# Images Vignette