Merge pull request #1825 from danforthcenter/image-sharpening

Image sharpening

Author: nfahlgren

docs/img/documentation_images/sharpen/sharp1.png

@@ -0,0 +1,44 @@
+## Sharpen
+
+Sharpens an image through the unsharp masking method. Applies a gaussian blur which is subtracted from an exaggerated version of the starting image.
+
+**plantcv.sharpen**(*img, ksize, amount=1, threshold=0, sigma_x=0, sigma_y=None, roi=None*)
+
+**returns** sharpened image
+
+- **Parameters:**
+    - img - RGB or grayscale image data
+    - ksize - Tuple of kernel dimensions, e.g. (5, 5). Must be odd integers.
+    - amount - Integer describing amount of sharpening, higher numbers will sharpen more.
+    - threshold - Integer cutoff on low contrast, contrasts lower than this will be removed.
+    - sigma_x - standard deviation in X direction; if 0 (default), calculated from kernel size
+    - sigma_y - standard deviation in Y direction; if sigma_Y is None (default), sigma_Y is taken to equal sigma_X
+    - roi - Optional rectangular ROI as returned by [`pcv.roi.rectangle`](roi_rectangle.md) within which to apply this function. (default = None, which uses the entire image)
+- **Context:**
+    - Used to reduce blur in an image
+
+**Original image**
+
+![Screenshot](img/documentation_images/threshold_2channels/VIS_TV_z500_h2_g0_e100_163042_0_m.png)
+
+**Sharpening Image**
+
+```python
+
+# Apply sharpening within an ROI to show differences
+roi = pcv.roi.rectangle(img, 200, 0, 335, 200)
+sharp1 = pcv.sharpen(img, (5, 5), amount=1, roi=roi)
+
+# Higher amount of sharpening will look more dramatic
+sharp5 = pcv.sharpen(img, (5, 5), amount = 5, roi=roi)
+```
+
+**Sharpen (ksize = (5,5), amount=1, roi=roi)**
+
+![sharp1](img/documentation_images/sharpen/sharp1.png)
+
+**Sharpen (ksize = (5,5), amount=5, roi=roi)**
+
+![sharp5](img/documentation_images/sharpen/sharp5.png)
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/main/plantcv/plantcv/sharpen.py)

docs/img/documentation_images/sharpen/sharp5.png

@@ -1156,6 +1156,10 @@ pages for more details on the input and output variable types.
 * post v3.0dev2: sr_img = **plantcv.scharr_filter**(*gray_img, dx, dy, scale*)
 * post v4.9: sr_img = **plantcv.scharr_filter**(*gray_img, dx, dy, scale, roi=None*)
 
+#### plantcv.sharpen
+* pre v5.0: NA
+* post v5.0: img = **plantcv.sharpen**(*img, ksize, amount=1, threshold=0, sigma_x=0, sigma_y=None, roi=None*)
+
 #### plantcv.shift_img
 
 * pre v3.0dev2: device, adjusted_img = **plantcv.shift_img**(*img, device, number, side="right", debug=None*)

docs/sharpen.md

@@ -160,6 +160,7 @@ nav:
         - 'Filter a mask by ROI (quickly)': roi_quick_filter.md
         - 'Convert ROI to Mask': roi2mask.md
       - 'Segment Image Series': segment_image_series.md
+      - 'Sharpen Image': sharpen.md
       - 'Shift Image': shift.md
       - 'Spatial Clustering': spatial_clustering.md
       - 'Spectral Index': spectral_index.md

docs/updating.md

@@ -4,17 +4,15 @@
 __version__ = version("plantcv")
 
 from plantcv.plantcv.fatal_error import fatal_error
-from plantcv.plantcv.classes import Params
-from plantcv.plantcv.classes import Outputs
 from plantcv.plantcv.classes import Spectral_data
 from plantcv.plantcv.classes import PSII_data
-from plantcv.plantcv.classes import Points
+from plantcv.plantcv.classes import Point
 from plantcv.plantcv.classes import Objects
 
 # Initialize an instance of the Params and Outputs class with default values
 # params and outputs are available when plantcv is imported
-params = Params()
-outputs = Outputs()
+from plantcv.plantcv._globals import Params, Outputs
+from plantcv.plantcv._globals import params, outputs
 
 from plantcv.plantcv.deprecation_warning import deprecation_warning
 from plantcv.plantcv.warn import warn
@@ -63,6 +61,7 @@
 from plantcv.plantcv.canny_edge_detect import canny_edge_detect
 from plantcv.plantcv.opening import opening
 from plantcv.plantcv.closing import closing
+from plantcv.plantcv.sharpen import sharpen
 from plantcv.plantcv import roi
 from plantcv.plantcv import threshold
 from plantcv.plantcv import visualize
@@ -87,12 +86,14 @@
 
 __all__ = [
     "fatal_error",
-    "Params",
-    "Outputs",
     "Spectral_data",
     'PSII_data',
-    'Points',
+    'Point',
     "Objects",
+    "Params",
+    "Outputs",
+    "params",
+    "outputs",
     "deprecation_warning",
     "warn",
     "print_image",
@@ -139,6 +140,7 @@
     "canny_edge_detect",
     "opening",
     "closing",
+    "sharpen",
     "roi",
     "threshold",
     "visualize",

mkdocs.yml

@@ -1,5 +1,5 @@
 # Debugging module
-from plantcv.plantcv import params
+from plantcv.plantcv._globals import params
 from plantcv.plantcv import print_image
 from plantcv.plantcv import plot_image