Merge pull request #1827 from danforthcenter/params-verbosity

Params verbosity

Author: nfahlgren

docs/Points.md

@@ -3,7 +3,7 @@
 Using [Jupyter Notebooks](jupyter.md) it is possible to interactively click to collect coordinates from an image, which can be used in various downstream applications. Left click on the image to collect a point. Right click removes the
 closest collected point.
 
-**plantcv.Points**(*img, figsize=(12, 6)*)
+**plantcv.Point**(*img, figsize=(12, 6)*)
 
 **returns** interactive image class
 
@@ -25,8 +25,8 @@ closest collected point.
 ```python
 from plantcv import plantcv as pcv
 
-# Create an instance of the Points class
-marker = pcv.Points(img=img, figsize=(12,6))
+# Create an instance of the Point class
+marker = pcv.Point(img=img, figsize=(12,6))
 
 # Click on the plotted image to collect coordinates
 

docs/params.md

@@ -50,7 +50,7 @@ the morphology sub-package. Default = 2.
 
 **saved_color_scale**: Using the `color_palette` function will save the color scale here for reuse in downstream functions. Set to `None` to remove. Default = `None`.
 
-**verbose**: Set the status of verboseness. When in "verbose" mode, the deprecation warning will always be printed once triggered. Default: `True`. Users can turn off deprecation warnings by setting `verbose=False`.
+**verbose**: Set the status of verboseness as an integer between 0 and 2. When in the most verbose mode (2), the deprecation warning will always be printed once triggered. Default: `1`. Users can turn off messages by setting `verbose=0` or opt for more messages/debug images with `verbose=2`.
 
 **unit**: Set the units of the size outputs. Users can scale size measurements by updating the `unit`, `px_height` and `px_width` Default: `pixels`
 

plantcv/plantcv/_debug.py

@@ -4,25 +4,33 @@
 from plantcv.plantcv import plot_image
 
 
-def _debug(visual, filename=None, **kwargs):
-    """
-    Save or display a visual for debugging.
+def _debug(visual, filename=None, verbosity_level=0, **kwargs):
+    """Save or display a visual for debugging.
 
-    Inputs:
-    visual   - An image or plot to display for debugging
-    filename - An optional filename to save the visual to (default: None)
-    kwargs - key-value arguments to xarray.plot method
+    Parameters
+    ----------
+    visual : numpy.ndarray
+        An image or plot to display for debugging
+    filename : str, optional
+        An optional filename to save the visual to (default: None)
+    verbosity_level : int, optional
+        Threshold for params.verbose to make debug image.
+        Defaults to 0, which essentially ignores params.verbose
+    **kwargs : dict
+        Key-value arguments to xarray.plot method
 
-    :param visual: numpy.ndarray
-    :param filename: str
-    :param kwargs: dict
+    Returns
+    -------
+    None
     """
-    # Auto-increment the device counter
-    params.device += 1
+    # if verbose from params is at least to the verbosity level, make debug images
+    if params.verbose >= verbosity_level:
+        # Auto-increment the device counter
+        params.device += 1
 
-    if params.debug == "print":
-        # If debug is print, save the image to a file
-        print_image(img=visual, filename=filename, **kwargs)
-    elif params.debug == "plot":
-        # If debug is plot, print to the plotting device
-        plot_image(img=visual, **kwargs)
+        if params.debug == "print":
+            # If debug is print, save the image to a file
+            print_image(img=visual, filename=filename, **kwargs)
+        elif params.debug == "plot":
+            # If debug is plot, print to the plotting device
+            plot_image(img=visual, **kwargs)

plantcv/plantcv/_globals.py

@@ -14,7 +14,7 @@ class Params:
     def __init__(self, device=0, debug=None, debug_outdir=".", line_thickness=5,
                  line_color=(255, 0, 255), dpi=100, text_size=0.55,
                  text_thickness=2, marker_size=60, color_scale="gist_rainbow", color_sequence="sequential",
-                 sample_label="default", saved_color_scale=None, verbose=True, unit="pixels", px_height=1, px_width=1):
+                 sample_label="default", saved_color_scale=None, verbose=1, unit="pixels", px_height=1, px_width=1):
         """Initialize parameters.
 
         Parameters
@@ -45,8 +45,8 @@ def __init__(self, device=0, debug=None, debug_outdir=".", line_thickness=5,
             Sample name prefix. Used in analyze functions. Default is "default".
         saved_color_scale : list, optional
             Saved color scale that will be applied next time color_palette is called. Default is None.
-        verbose : bool
-            Whether or not in verbose mode. Default is True.
+        verbose : int
+            0:2 representing verbosity level. 0 is least verbose, 2 is most verbose. Default is 1.
         unit : str
             Units of size trait outputs. Default is "pixels".
         px_height : float

plantcv/plantcv/deprecation_warning.py

@@ -6,14 +6,15 @@
 
 
 def deprecation_warning(warning):
-    """Print out deprecation warning
+    """Print out deprecation warning.
 
-    Inputs:
-    warning = warning message text
-
-    :param warning: str
+    Parameters
+    ----------
+    warning : str
+        The warning message text.
     """
-    v = version("plantcv")
-    warning_msg = f"DeprecationWarning: {warning} Current PlantCV version: {v}"
-    if params.verbose is True:
+    if params.verbose == 2:
+        v = version("plantcv")
+        warning_msg = f"DeprecationWarning: {warning} Current PlantCV version: {v}"
+
         print(warning_msg, file=sys.stderr)

tests/plantcv/test_deprecation_warning.py

@@ -1,8 +1,10 @@
-from plantcv.plantcv import deprecation_warning
+from plantcv.plantcv._globals import params
+from plantcv.plantcv.deprecation_warning import deprecation_warning
 
 
 def test_deprecation_warning():
     """Test for PlantCV."""
     # Verify that the fatal_error function raises a RuntimeError
+    params.verbose = 2
     deprecation_warning("This is just a test, and it's just a warning")
     assert True