Merge branch 'code-laurent-20230418' into devel

Author: ehrenfeu

CHANGELOG.md

@@ -9,6 +9,20 @@
 * `pathtools.join2` can be used to join paths, much like `os.path.join` except
   that it will work with `java.io.File` objects as well (but doesn't support
   more than two path components / parameters).
+* `resultstable` sub-module with the following functions:
+  * `add_results_to_resultstable`
+  * `get_resultstable`
+  * `preset_results_column`
+* `misc.timed_log` for printing log messages with a timestamp.
+* Several functions in the `misc` submodule:
+  * `calculate_mean_and_stdv`
+  * `elapsed_time_since`
+  * `find_focus`
+  * `get_free_memory`
+  * `percentage`
+  * `progressbar`
+  * `setup_clean_ij_environment`
+  * `timed_log`
 
 ### Changed
 

src/imcflibs/imagej/bioformats.py

@@ -137,7 +137,7 @@ def export(imp, filename, overwrite=False):
 
     Parameters
     ----------
-    imp : ImagePlus
+    imp : ij.ImagePlus
         The ImagePlus object to be exported by Bio-Formats.
     filename : str
         The output filename, may include a full path.
@@ -178,7 +178,7 @@ def export_using_orig_name(imp, path, orig_name, tag, suffix, overwrite=False):
 
     Parameters
     ----------
-    imp : ImagePlus
+    imp : ij.ImagePlus
         The ImagePlus object to be exported by Bio-Formats.
     path : str or object that can be cast to a str
         The output path.

src/imcflibs/imagej/gpu.py

@@ -8,9 +8,9 @@ def erode_labels(clij2_instance, label_image, erosion_radius, channel=None):
 
     Parameters
     ----------
-    clij2_instance : clij2_instance
+    clij2_instance : net.haesleinhuepf.clij.CLIJ
         Instance of CLIJ to communicate with the GPU.
-    label_image : ImagePlus
+    label_image : ij.ImagePlus
         Label image to be eroded.
     erosion_radius : int
         Radius for erosion.
@@ -19,15 +19,14 @@ def erode_labels(clij2_instance, label_image, erosion_radius, channel=None):
 
     Returns
     -------
-    ImagePlus
+    ij.ImagePlus
         Label image with eroded labels.
     """
 
     list_of_images = []
     channel_list = [channel] if channel else range(1, label_image.getNChannels() + 1)
 
     for channel in channel_list:
-
         current_channel = Duplicator().run(
             label_image,
             channel,
@@ -59,9 +58,9 @@ def dilate_labels(clij2_instance, label_image, dilation_radius, channel=None):
 
     Parameters
     ----------
-    clij2_instance : clij2_instance
+    clij2_instance : net.haesleinhuepf.clij.CLIJ
         Instance of CLIJ to communicate with the GPU.
-    label_image : ImagePlus
+    label_image : ij.ImagePlus
         Label Image to be dilated.
     erosion_radius : int
         Radius for dilation.
@@ -70,7 +69,7 @@ def dilate_labels(clij2_instance, label_image, dilation_radius, channel=None):
 
     Returns
     -------
-    ImagePlus
+    ij.ImagePlus
         Label image with dilated labels.
     """
 
@@ -114,16 +113,16 @@ def merge_labels(clij2_instance, label_image, channel=None):
 
     Parameters
     ----------
-    clij2_instance : clij2_instance
+    clij2_instance : net.haesleinhuepf.clij.CLIJ
         Instance of CLIJ to communicate with the GPU.
-    label_image : ImagePlus
+    label_image : ij.ImagePlus
         Label image with touching labels.
     channel : int, optional
         Specific channel to apply label merging.
 
     Returns
     -------
-    ImagePlus
+    ij.ImagePlus
         New ImagePlus with merged labels.
     """
 
@@ -135,7 +134,6 @@ def merge_labels(clij2_instance, label_image, channel=None):
         channel_list = [channel]
 
     for channel in channel_list:
-
         current_channel = Duplicator().run(
             label_image,
             channel,

src/imcflibs/imagej/labelimage.py

@@ -1,21 +1,19 @@
 """Functions to work with ImageJ label images."""
 
-# pylint: disable-msg=import-error
-
 from ij import IJ, ImagePlus, Prefs
 from ij.plugin import Duplicator, ImageCalculator
+from ij.plugin.filter import ImageProcessor, ThresholdToSelection
 from ij.process import FloatProcessor, ImageProcessor
-from ij.plugin.filter import ThresholdToSelection
-
 from inra.ijpb.label import LabelImages as li
 from inra.ijpb.plugins import AnalyzeRegions
 
+
 def label_image_to_roi_list(label_image, low_thresh=None):
     """Converts a label image to a list of ROIs
 
     Parameters
     ----------
-    label_image : ImagePlus
+    label_image : ij.ImagePlus
         Label image to convert
     low_thresh : int, optional
         Value under which the labels should be discarded, by default None
@@ -73,14 +71,14 @@ def relate_label_images(label_image_ref, label_image_to_relate):
 
     Parameters
     ----------
-    label_image_ref : ImagePlus
+    label_image_ref : ij.ImagePlus
         Reference to use for the labels
-    label_image_to_relate : ImagePlus
+    label_image_to_relate : ij.ImagePlus
         Image to change for the labels
 
     Returns
     -------
-    ImagePlus
+    ij.ImagePlus
         New ImagePlus with modified labels matching the reference
     """
 
@@ -97,7 +95,7 @@ def filter_objects(label_image, table, string, min_val, max_val):
 
     Parameters
     ----------
-    label_image : ImagePlus
+    label_image : ij.ImagePlus
         Label image on which to filter
     table : ResultsTable
         ResultsTable containing all the measurements on which to filter
@@ -111,7 +109,7 @@ def filter_objects(label_image, table, string, min_val, max_val):
 
     Returns
     -------
-    ImagePlus
+    ij.ImagePlus
         Label image containing only the remaining labels
     """
 
@@ -129,7 +127,7 @@ def measure_objects_size_shape_2d(label_image):
 
     Parameters
     ----------
-    label_image : ImagePlus
+    label_image : ij.ImagePlus
         Label image on which to get the shapes
 
     Returns

src/imcflibs/imagej/misc.py

@@ -4,8 +4,8 @@
 import time
 
 from ij import IJ  # pylint: disable-msg=import-error
-from ij.plugin.frame import RoiManager  # pylint: disable-msg=import-error
 from ij.measure import ResultsTable  # pylint: disable-msg=import-error
+from ij.plugin.frame import RoiManager  # pylint: disable-msg=import-error
 
 from ..log import LOG as log
 
@@ -30,19 +30,18 @@ def error_exit(msg):
 
 
 def elapsed_time_since(start, end=None):
-    """Prints the elapsed time for execution
+    """Generate a string with the time elapsed between the two timepoints.
 
     Parameters
     ----------
-    start : time
-        Start time
-    end : time, optional
-        End time
+    start : time.time
+        Start time.
+    end : time.time, optional
+        End time. If skipped the current time will be used.
 
     Returns
     -------
     str
-        Formatted time elapsed
     """
 
     if not end:
@@ -54,19 +53,18 @@ def elapsed_time_since(start, end=None):
 
 
 def percentage(part, whole):
-    """Returns the percentage of a value based on total
+    """Calculate the percentage of a value based on total.
 
     Parameters
     ----------
     part : float
-        Part
+        Part.
     whole : float
-        Complete size
+        Complete size.
 
     Returns
     -------
     float
-        Percentage
     """
     return 100 * float(part) / float(whole)
 
@@ -82,7 +80,7 @@ def calculate_mean_and_stdv(float_values):
     Returns
     -------
     [float, float]
-        Mean and standard deviation of the list.
+        Mean (1st item) and standard deviation (2nd item) of the list.
     """
     mean = sum(float_values) / len(float_values)
     tot = 0.0
@@ -92,17 +90,21 @@ def calculate_mean_and_stdv(float_values):
 
 
 def find_focus(imp):
-    """Function to get the focused stack. Works on single-channel images only.
+    """Find the slice of a stack that seems to bet the best focused one.
+
+    NOTE: currently only single-channel stacks are supported.
+
+    FIXME: explain what the function is actually doing, i.e. how does it decide
+    what "the best focused one" is?
 
     Parameters
     ----------
-    imp : ImagePlus
+    imp : ij.ImagePlus
         A single-channel ImagePlus.
 
     Returns
     -------
     int
-        Slice number which seems to be the best focused one.
     """
 
     imp_dimensions = imp.getDimensions()
@@ -138,8 +140,8 @@ def find_focus(imp):
 def progressbar(progress, total, line_number, prefix=""):
     """Progress bar for the IJ log window.
 
-    FIXME: how is this different from show_progressbar() above? Please explain
-    in the function description here.
+    Show a progress bar in the log window of Fiji at a specific line independent
+    of the main Fiji progress bar.
 
     Parameters
     ----------
@@ -153,14 +155,34 @@ def progressbar(progress, total, line_number, prefix=""):
         Text to use before the progress bar, by default ''.
     """
 
-    size = 30
+    size = 20
     x = int(size * progress / total)
     IJ.log(
         "\\Update%i:%s[%s%s] %i/%i\r"
-        % (line_number, prefix, "#" * x, "." * (size - x), progress, total)
+        % (
+            line_number,
+            timed_log(prefix, True),
+            "#" * x,
+            "." * (size - x),
+            progress,
+            total,
+        )
     )
 
 
+def timed_log(message, as_string=False):
+    """Print a message to the ImageJ log window with a timestamp added.
+
+    Parameters
+    ----------
+    message : str
+        Message to print
+    """
+    if as_string:
+        return time.strftime("%H:%M:%S", time.localtime()) + ": " + message + " "
+    IJ.log(time.strftime("%H:%M:%S", time.localtime()) + ": " + message + " ")
+
+
 def get_free_memory():
     """Get the free memory thats available to ImageJ.
 
@@ -186,16 +208,11 @@ def setup_clean_ij_environment(rm=None, rt=None):
     rt : ResultsTable, optional
         A reference to an IJ-ResultsTable instance.
     """
-    # FIXME: use function(s) from the "roimanager" module!
     if not rm:
-        rm = RoiManager.getInstance()
-        if not rm:
-            rm = RoiManager()
+        rm = roimanager.get_roimanager()
 
     if not rt:
-        rt = ResultsTable.getInstance()
-        if not rt:
-            rt = ResultsTable()
+        rt = resultstable.get_resultstable()
 
     rm.runCommand("reset")
     rt.reset()