Merge pull request #910 from danforthcenter/cmyk_doc_updates

Doc updates
danforthcenter · Jun 16, 2022 · deb0ffd · deb0ffd
2 parents 811e655 + 5507652
commit deb0ffd
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Showing 15 changed files with 45 additions and 21 deletions.
diff --git a/docs/apply_transformation_matrix.md b/docs/apply_transformation_matrix.md
@@ -40,3 +40,4 @@ corrected_img = pcv.transform.apply_transformation_matrix(source_img=source_img,
 
 ![Screenshot](img/documentation_images/correct_color_imgs/hstack.jpg)
 
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/transform/color_correction.py)
diff --git a/docs/create_color_card_mask.md b/docs/create_color_card_mask.md
@@ -37,3 +37,5 @@ mask = pcv.transform.create_color_card_mask(rgb_img=img, radius=10, start_coord=
 **Color card mask**
 
 ![Screenshot](img/documentation_images/correct_color_imgs/color_card_mask.jpg)
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/transform/color_correction.py)
diff --git a/docs/find_color_card.md b/docs/find_color_card.md
@@ -51,3 +51,5 @@ avg_chip_size = pcv.outputs.observations['prefix']['color_chip_size']['value']
 **Tilted color card**
 
 ![Screenshot](img/documentation_images/correct_color_imgs/tilted_color_card.jpg)
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/transform/color_correction.py)
diff --git a/docs/get_color_matrix.md b/docs/get_color_matrix.md
@@ -55,3 +55,4 @@ print(color_matrix)
      [ 220.       74.632   158.8224  144.3724]]
 
 ```
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/transform/color_correction.py)
diff --git a/docs/load_matrix.md b/docs/load_matrix.md
@@ -24,3 +24,4 @@ filename = "test.npz"
 matrix = pcv.transform.load_matrix(filename=filename)
 
 ```
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/transform/color_correction.py)
diff --git a/docs/mp_inverse.md b/docs/mp_inverse.md
@@ -26,3 +26,4 @@ print(matrix_m)
 
 ```
 
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/transform/color_correction.py)
diff --git a/docs/otsu_threshold.md b/docs/otsu_threshold.md
@@ -28,8 +28,8 @@ from plantcv import plantcv as pcv
 pcv.params.debug = "print"
 
 # Create binary image from a gray image based on threshold values. 
-# Targeting light objects in the image.
-threshold_light = pcv.threshold.otsu(gray_img=gray_img, max_value=255, object_type='dark')
+# Targeting dark objects in the image.
+threshold_dark = pcv.threshold.otsu(gray_img=gray_img, max_value=255, object_type='dark')
 
 ```
 
@@ -44,8 +44,8 @@ threshold_light = pcv.threshold.otsu(gray_img=gray_img, max_value=255, object_ty
 ```python
 
 # Create binary image from a gray image based on threshold values. 
-# Targeting dark objects in the image.
-threshold_dark = pcv.threshold.otsu(gray_img=gray_img, max_value=255, object_type='light')
+# Targeting light objects in the image.
+threshold_light = pcv.threshold.otsu(gray_img=gray_img, max_value=255, object_type='light')
 
 ```
 

diff --git a/docs/parallel_config.md b/docs/parallel_config.md
@@ -207,3 +207,6 @@ Windows you will need to specify the whole path to `plantcv-workflow.py`.
 ```shell
 python %CONDA_PREFIX%/Scripts/plantcv-workflow.py --config my_config.json
 ```
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/parallel/__init__.py)
+
diff --git a/docs/rgb2cmyk.md b/docs/rgb2cmyk.md
@@ -26,9 +26,8 @@ from plantcv import plantcv as pcv
 # or "plot" (Jupyter Notebooks or X11)
 pcv.params.debug = "print"
 
-# image converted from RGB to LAB, channels are then split. 
-# Lightness ('l') channel is output
-l_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='Y')
+# image converted from RGB to CMYK, channels are then split. 
+y_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='Y')
 
 ```
 
@@ -38,8 +37,8 @@ l_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='Y')
 
 ```python
 
-# Green-Magenta ('a') channel is output
-a_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='C')
+# Cyan ('c') channel is output
+c_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='C')
 
 ```
 
@@ -49,8 +48,8 @@ a_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='C')
 
 ```python
 
-# Green-Magenta ('a') channel is output
-a_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='M')
+# Magenta ('m') channel is output
+m_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='M')
 
 ```
 
@@ -60,8 +59,8 @@ a_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='M')
 
 ```python
 
-# Green-Magenta ('a') channel is output
-a_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='Y')
+# Yellow ('a') channel is output
+y_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='Y')
 
 ```
 
@@ -71,7 +70,9 @@ a_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='Y')
 
 ```python
 
-# Green-Magenta ('a') channel is output
-a_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='K')
+# Black ('k') channel is output
+k_channel = pcv.rgb2gray_cmyk(rgb_img=rgb_img, channel='K')
 
 ```
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/rgb2gray_cmyk.py)
diff --git a/docs/save_matrix.md b/docs/save_matrix.md
@@ -26,3 +26,5 @@ pcv.transform.save_matrix(matrix=matrix, filename=fname)
 
 ```
 
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/transform/color_correction.py)
+
diff --git a/docs/texture_threshold.md b/docs/texture_threshold.md
@@ -24,7 +24,7 @@ texture calculation for thresholding.
 - **Note:**
     - This function is computationally expensive and will likely take several minutes to run (even longer if images are large).
 - **Example use:**
-    - [Interactive Documentation](https://mybinder.org/v2/gh/danforthcenter/plantcv-binder.git/master?filepath=notebooks%2Fthreshold.ipynb)
+    - Below
 
 **Original image (lightness channel)**
 

diff --git a/docs/transform_correct_color.md b/docs/transform_correct_color.md
@@ -58,3 +58,4 @@ target_matrix, source_matrix, transformation_matrix, corrected_img = pcv.transfo
 
 ![Screenshot](img/documentation_images/correct_color_imgs/hstack.jpg)
 
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/transform/color_correction.py)
diff --git a/docs/transform_resize.md b/docs/transform_resize.md
@@ -69,19 +69,24 @@ resize_img5 = pcv.transform.resize_factor(img=img, factors=(0.1154905775, 0.1154
 ```
 
 **Images after resizing**
-1st resized image
+**1st resized image (default interpolation)
+
 ![Screenshot](img/documentation_images/resize/19_resize1.jpg)
 
-2nd resized image
+**2nd resized image (Interpolation by nearest)**
+
 ![Screenshot](img/documentation_images/resize/19_resize2.jpg)
 
-3rd resized image (cropping)
+**3rd resized image (cropping)**
+
 ![Screenshot](img/documentation_images/resize/19_resize3.jpg)
 
-3rd resized image (zero-padding)
+**4th resized image (zero-padding)**
+
 ![Screenshot](img/documentation_images/resize/19_resize4.jpg)
 
-5th resize image
+**5th resized image (by factor)**
+
 ![Screenshot](img/documentation_images/resize/19_resize5.jpg)
 
 **Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/transform/resize.py)
diff --git a/docs/transformation_matrix.md b/docs/transformation_matrix.md
@@ -25,3 +25,4 @@ deviance, transformation_matrix = pcv.transform.calc_transformation_matrix(matri
 
 ```
 
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/transform/color_correction.py)
diff --git a/docs/visualize_pseudocolor.md b/docs/visualize_pseudocolor.md
@@ -38,6 +38,7 @@ unaltered, the  matplotlib default DPI is 100 pixels per inch.
 ![Screenshot](img/documentation_images/pseudocolor/mask.jpg)
 
 **Mask of "bad" values**
+
 ![Screenshot](img/documentation_images/pseudocolor/bad_mask.png)
 
 
@@ -109,9 +110,11 @@ pseudo_img_mask_obj_bad_mask = pcv.visualize.pseudocolor(gray_img=img, obj=obg,
 ![Screenshot](img/documentation_images/pseudocolor/pseudo_onimage_simple.jpg)
 
 **Pseudocolored, Pixels With User Defined "bad" Values Marked Using Red Color (no axes or colorbar)**
+
 ![Screenshot](img/documentation_images/pseudocolor/pseudocolored_mask_bad.png)
 
 **Pseudocolored, Cropped, background="white", Pixels With User Defined "bad" Values Marked Using Red Color (no axes)**
+
 ![Screenshot](img/documentation_images/pseudocolor/pseudocolored_mask_bad_obj.png)
 
 **Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/master/plantcv/plantcv/visualize/pseudocolor.py)