img before objects in order, start adding doc page

docs/analyze_stem.md

@@ -0,0 +1,24 @@
+## Analyze Stem Objects
+
+Primary, or stem, objects identified during workflows that examine the [mmorphology](morphology_tutorial.md) of 
+plants or plant organs can have specific characteristics measured about the stem segments of a skeleton. These measurement
+
+**plantcv.morphology.analyze_stem**(*img, obj, mask*)
+
+**returns** analysis_image
+
+- **Parameters:**
+    - img - RGB or grayscale image data for plotting.
+    - obj - Single or grouped contour object.
+    - mask - Binary image to use as mask for moments analysis.
+- **Context:**
+    - Used to output shape characteristics of an image, including height, object area, convex hull, convex hull area, 
+    perimeter, extent x, extent y, longest axis, centroid x coordinate, centroid y coordinate, in bounds QC (if object 
+    touches edge of image, image is flagged). 
+- **Example use:**
+    - [Use In VIS Tutorial](vis_tutorial.md)
+
+
+- **Output data stored:** Data ('stem_angle', 'stem_height', and 'stem_length') 
+    automatically gets stored to the [`Outputs` class](outputs.md) when this function is ran. 
+    These data can always get accessed during a workflow. For more detail about data output see [Summary of Output Observations](output_measurements.md#summary-of-output-observations)

plantcv/plantcv/morphology/analyze_stem.py

@@ -9,19 +9,19 @@
 from plantcv.plantcv import print_image
 
 
-def analyze_stem(stem_objects, rgb_img):
+def analyze_stem(rgb_img, stem_objects):
     """ Calculate angle of segments (in degrees) by fitting a linear regression line to segments.
 
         Inputs:
-        stem_objects  = List of stem segments (output from segment_sort function)
         rgb_img       = RGB image to plot debug image
+        stem_objects  = List of stem segments (output from segment_sort function)
 
         Returns:
         labeled_img    = Stem analysis debugging image
 
 
-        :param stem_objects: list
         :param rgb_img: numpy.ndarray
+        :param stem_objects: list
         :return labeled_img: numpy.ndarray
         """