Add cursors module #48

schutyb · 2024-03-26T22:48:41Z

Description

Cursors module to select component in regions
1- For circular selection
2- For to selec component in linear ranges
...

Release note

Summarize the changes in the code block below to be included in the
release notes:

...

Checklist

The pull request title, summary, and description are concise.
Related issues are linked in the description.
New dependencies are explained.
The source code and documentation can be distributed under the MIT license.
The source code adheres to code standards.
New classes, functions, and features are thoroughly tested.
New, user-facing classes, functions, and features are documented.
New features are covered in tutorials.
No files other than source code, documentation, and project settings are added to the repository.

schutyb · 2024-03-26T23:40:10Z

Hi @cgohlke I have this error with:

Run python -m black --check cursors.py
would reformat /home/runner/work/phasorpy/phasorpy/src/phasorpy/cursors.py

Oh no! 💥 💔 💥
1 file would be reformatted, 19 files would be left unchanged.
Error: Process completed with exit code 1.

And I thoght it was due to: single quotes and lines up to 79 characters are allowed, but I checked all the lines and there is no line over 79 characters.

I there anything am I missing?

Thanks

cgohlke · 2024-03-26T23:58:50Z

Just run python -m black . in your local branch before committing.

cgohlke · 2024-03-27T14:13:32Z

Let us know when this PR is ready to be reviewed.

schutyb · 2024-03-27T14:14:42Z

Just run python -m black . in your local branch before committing.

Thanks, It worked now, so without "check" the "black" command correct the mistakes, right?

schutyb · 2024-03-27T14:16:13Z

Let us know when this PR is ready to be reviewed.

You can do it now

src/phasorpy/cursors.py

cgohlke · 2024-03-27T15:27:46Z

src/phasorpy/cursors.py

+  - :py:func:`circular_cursor`
+  - :py:func:`range_cursor`
+
+


Maybe give a preview of what other functions/functionalities are going to be in this module?

src/phasorpy/cursors.py

cgohlke · 2024-03-27T16:43:47Z

tests/test_cursors.py

+    center = numpy.array([[-0.5, -0.5], [-0.5, 0.5], [0.5, -0.5], [0.5, 0.5]])
+    radius = [0.1, 0.1, 0.1, 0.1]
+    mask = circular_cursor(real, imag, center, radius=radius, components=4)
+    assert_array_equal(mask, [1., 2., 3., 4.])


This file does not seem to be formatted with black?

cgohlke · 2024-03-27T16:50:26Z

src/phasorpy/cursors.py

+- use cursors to select region of interest in the phasor:
+
+  - :py:func:`circular_cursor`
+  - :py:func:`range_cursor`


range_cursor does not seem to operate on phasor coordinates (?)

cgohlke · 2024-03-27T16:53:13Z

src/phasorpy/cursors.py

+
+    Examples
+    --------
+    Compute the range cursor:


Add blank line after.

src/phasorpy/cursors.py

cgohlke · 2024-04-11T17:12:51Z

In this case we obtained a LUT with dim=mxnx3

In what sense is this a lookup table? This kind of data is usually encoded as a bit-field...

It looks like none of us has a clear idea of what (and why) is the best "cursors" data structure for phasor analysis and visualization. Lets discuss on Monday. So far the options are labels and bit-fields. A 2-dimensional LUT (indexed with s and g) is another option.

I propose to finish this PR (address all comments and pass tests) so it can be used already. Since we might want to add other data structures and shapes later, maybe rename the functions to something like label_from_phasor_circular and label_from_ranges.

schutyb · 2024-04-12T23:16:25Z

In this case we obtained a LUT with dim=mxnx3

In what sense is this a lookup table? This kind of data is usually encoded as a bit-field...

I didn´t know about bit-field, I read about it now, and you are right. Let talk on monday about it!

It looks like none of us has a clear idea of what (and why) is the best "cursors" data structure for phasor analysis and visualization. Lets discuss on Monday. So far the options are labels and bit-fields. A 2-dimensional LUT (indexed with s and g) is another option.

I propose to finish this PR (address all comments and pass tests) so it can be used already. Since we might want to add other data structures and shapes later, maybe rename the functions to something like label_from_phasor_circular and label_from_ranges.

Great, I´ll work on monday after we talk, we have the workshop next week at the unit and I still need to finish some things for my presentation this weekend.

schutyb · 2024-04-29T15:06:13Z

@cgohlke all tests passed, it is ready for review

cgohlke · 2024-04-29T15:27:38Z

Can you merge the main branch and mark open conversations as resolved if they were addressed?

schutyb · 2024-04-29T15:32:22Z

Can you merge the main branch and mark open conversations as resolved if they were addressed?

I cannot merge, bc I need one approving review

cgohlke · 2024-04-29T15:43:49Z

What I meant was to merge/pull the current main branch (which contains over a month of changes) into your cursors branch.

cgohlke · 2024-04-29T22:47:20Z

Several of the previous comments have not been addressed and the tutorial needs to be tidied. See the patch below for suggested changes.

I strongly recommend to exclude upper range values from the ranges. It is the default in Python and numpy, and no warning is printed in the tutorial.

The types of the returned arrays should be uint8 or uint16 based on the number of labels. More labels should probably raise an error or use uint32/uint64 if you think there is a possible use case.

Both cursor function are inefficient. This can be changed later. I still think the range cursor could be implemented using numpy.digitize. Did you try?

diff --git a/docs/api/index.rst b/docs/api/index.rst
index d9314d6..c20663c 100644
--- a/docs/api/index.rst
+++ b/docs/api/index.rst
@@ -14,6 +14,7 @@ PhasorPy library version |version|.
 
     phasorpy
     phasor
+    cursors
     components
     plot
     io
@@ -21,4 +22,3 @@ PhasorPy library version |version|.
     datasets
     utils
     cli
-    cursors
diff --git a/src/phasorpy/cursors.py b/src/phasorpy/cursors.py
index 1a51a13..728260f 100644
--- a/src/phasorpy/cursors.py
+++ b/src/phasorpy/cursors.py
@@ -1,10 +1,11 @@
-""" Select phasor coordinates.
-    The ``phasorpy.cursors`` module provides functions to:
+"""Select phasor coordinates.
+
+The ``phasorpy.cursors`` module provides functions to:
 
 - create labels for region of interests in the phasor space:
 
-  - :py:func:`circular_cursor`
-  - :py:func:`range_cursor`
+  - :py:func:`label_from_phasor_circular`
+  - :py:func:`label_from_ranges`
 
 """
 
@@ -30,12 +31,14 @@ import numpy
 
 
 def label_from_phasor_circular(
-    real,
-    imag,
+    real: ArrayLike,
+    imag: ArrayLike,
+    /,
     center: ArrayLike,
     radius: ArrayLike,
 ) -> NDArray[Any]:
     r"""Return indices of circle to which each phasor coordinate belongs.
+
     Phasor coordinates that do not fall in a circle have an index of zero.
 
     Parameters
@@ -64,11 +67,14 @@ def label_from_phasor_circular(
     --------
     Compute label array for four circles:
 
-    >>> label_from_phasor_circular(numpy.array([-0.5, -0.5, 0.5, 0.5]),
-    ...     numpy.array([-0.5, 0.5, -0.5, 0.5]),
-    ...     numpy.array([[-0.5, -0.5], [-0.5, 0.5], [0.5, -0.5], [0.5, 0.5]]),
-    ...     radius=[0.1, 0.1, 0.1, 0.1])
-    array([1, 2, 3, 4])
+    >>> label_from_phasor_circular(
+    ...     [-0.5, -0.5, 0.5, 0.5],
+    ...     [-0.5, 0.5, -0.5, 0.5],
+    ...     center=[[-0.5, -0.5], [-0.5, 0.5], [0.5, -0.5], [0.5, 0.5]],
+    ...     radius=[0.1, 0.1, 0.1, 0.1]
+    ... )
+    array([1, 2, 3, 4], dtype=uint8)
+
     """
     real = numpy.asarray(real)
     imag = numpy.asarray(imag)
@@ -77,29 +83,37 @@ def label_from_phasor_circular(
 
     if real.shape != imag.shape:
         raise ValueError(f'{real.shape=} != {imag.shape=}')
+    if center.ndim != 2 or center.shape[1] != 2:
+        raise ValueError(f'invalid {center.shape=}')
+    if radius.ndim != 1 or radius.shape != (center.shape[0],):
+        raise ValueError(f'invalid {radius.shape=}')
     if numpy.any(radius < 0):
         raise ValueError('radius is < 0')
-    label = numpy.zeros(real.shape, dtype=numpy.int8)
+
+    dtype = numpy.uint8 if len(center) < 256 else numpy.uint16
+    label = numpy.zeros(real.shape, dtype=dtype)
     for i in range(len(center)):
         condition = (
-            (real - center[i][0]) ** 2
-            + (imag - center[i][1]) ** 2
-            - radius[i] ** 2
+            numpy.square(real - center[i][0])
+            + numpy.square(imag - center[i][1])
+            - numpy.square(radius[i])
         )
         label = numpy.where(
-            condition > 0, label, numpy.ones(label.shape) * (i + 1)
+            condition > 0, label, numpy.full(label.shape, i + 1, dtype=dtype)
         )
     return label
 
 
-def label_from_ranges(values, ranges: ArrayLike) -> NDArray[Any]:
+def label_from_ranges(values: ArrayLike, /, ranges: ArrayLike) -> NDArray[Any]:
     r"""Return indices of range to which each value belongs.
+
     Values that do not fall in any range have an index of zero.
 
     Parameters
     ----------
-    values : array_like, shape (M, 2)
-    ranges : array_like
+    values : array_like
+        Values to be labeled.
+    ranges : array_like, shape (M, 2)
         Start and stop values of ranges.
 
     Returns
@@ -114,52 +128,60 @@ def label_from_ranges(values, ranges: ArrayLike) -> NDArray[Any]:
 
     Examples
     --------
-    Compute the range cursor:
+    Compute label array for three ranges:
+
+    >>> label_from_ranges(
+    ...     [[3.3, 6, 8], [15, 20, 7]], ranges=[(2, 8), (10, 15), (20, 25)]
+    ... )
+    array([[1, 1, 0], [0, 3, 1]], dtype=uint8)
 
-    >>> label_from_ranges(numpy.array([[3.3, 6, 8], [15, 20, 7]]),
-    ...     numpy.array([(2, 8), (10, 15), (20, 25)]))
-    array([[1, 1, 1], [2, 3, 1]])
     """
     values = numpy.asarray(values)
     ranges = numpy.asarray(ranges)
+    if ranges.ndim != 2 or ranges.shape[1] != 2:
+        raise ValueError(f'invalid {ranges.shape=}')
 
     if _overlapping_ranges(ranges):
-        warnings.warn("Overlapping ranges", UserWarning)
-    label = numpy.zeros_like(values, dtype=int)
+        warnings.warn('Overlapping ranges', UserWarning)
+
+    dtype = numpy.uint8 if ranges.shape[0] < 256 else numpy.uint16
+    label = numpy.zeros_like(values, dtype=dtype)
     # Iterate over each value in the array
     for index, value in numpy.ndenumerate(values):
         # Iterate over each range
         for range_index, (start, end) in enumerate(ranges):
             # Check if the value falls within the current range
-            if start <= value <= end:
+            if start <= value < end:
                 # Set the index of the current range
                 label[index] = range_index + 1
                 break
     return label
 
 
-def _overlapping_ranges(ranges) -> bool:
+def _overlapping_ranges(ranges: ArrayLike) -> bool:
     r"""Check if there are overlapping ranges in an array of ranges.
 
     Parameters
     ----------
-        ranges : array_like
-            Start and stop values of ranges.
+    ranges : array_like
+        Start and stop values of ranges.
 
     Returns
     -------
-        bool: True if there are overlapping ranges, False otherwise.
+    bool: True if there are overlapping ranges, False otherwise.
 
     Example
     -------
-    Compute for some range with overlapping.
-        >>> _overlapping_ranges([(1, 5), (3, 8), (6, 10), (9, 12)])
-        True
+    Compute for some range with overlapping:
+
+    >>> _overlapping_ranges([(1, 5), (3, 8), (6, 10), (9, 12)])
+    True
+
     """
     ranges = numpy.asarray(ranges)
     for i in range(len(ranges)):
         for j in range(i + 1, len(ranges)):
             # Check if the ranges overlap
-            if ranges[i][0] <= ranges[j][1] and ranges[j][0] <= ranges[i][1]:
+            if ranges[i][0] < ranges[j][1] and ranges[j][0] < ranges[i][1]:
                 return True  # Ranges overlap
     return False  # No overlaps found
diff --git a/tests/test_cursors.py b/tests/test_cursors.py
index 3339ad8..1e27354 100644
--- a/tests/test_cursors.py
+++ b/tests/test_cursors.py
@@ -13,11 +13,12 @@ def test_label_from_phasor_circular():
     imag = numpy.array([-0.5, 0.5, -0.5, 0.5])
     center = numpy.array([[-0.5, -0.5], [-0.5, 0.5], [0.5, -0.5], [0.5, 0.5]])
     radius = [0.1, 0.1, 0.1, 0.1]
-    mask = label_from_phasor_circular(real, imag, center, radius=radius)
-    assert_array_equal(mask, [1.0, 2.0, 3.0, 4.0])
+    labels = label_from_phasor_circular(real, imag, center, radius=radius)
+    assert labels.dtype == 'uint8'
+    assert_array_equal(labels, [1.0, 2.0, 3.0, 4.0])
 
 
-def test_label_from_phasor_circular_ValueErros():
+def test_label_from_phasor_circular_errors():
     # Test ValueErrors
     real = numpy.array([-0.5, -0.5, 0.5, 0.5])
     imag = numpy.array([-0.5, 0.5, -0.5, 0.5])
@@ -37,5 +38,6 @@ def test_label_from_ranges():
     # Test label from ranges
     values = numpy.array([[3.3, 6, 8], [15, 20, 7]])
     ranges = numpy.array([(2, 8), (10, 15), (20, 25)])
-    mask = label_from_ranges(values, ranges)
-    assert_array_equal(mask, [[1, 1, 1], [2, 3, 1]])
+    labels = label_from_ranges(values, ranges)
+    assert labels.dtype == 'uint8'
+    assert_array_equal(labels, [[1, 1, 0], [0, 3, 1]])
diff --git a/tutorials/phasorpy_cursors.py b/tutorials/phasorpy_cursors.py
index 2c782f8..2bf59ab 100644
--- a/tutorials/phasorpy_cursors.py
+++ b/tutorials/phasorpy_cursors.py
@@ -1,8 +1,8 @@
 """
-Phasor Cursors selectors
-========================
+Phasor cursors
+==============
 
-An introduction to cursors module.
+An introduction to selecting phasor coordinates using cursors.
 
 """
 
@@ -11,8 +11,8 @@ An introduction to cursors module.
 
 import math
 
-import numpy
 import tifffile
+from matplotlib import pyplot
 
 from phasorpy.cursors import label_from_phasor_circular, label_from_ranges
 from phasorpy.datasets import fetch
@@ -20,80 +20,83 @@ from phasorpy.phasor import phasor_from_signal, phasor_to_polar
 from phasorpy.plot import PhasorPlot
 
 # %%
-# Using circular cursors
-# ----------------------
+# Circular cursors
+# ----------------
 #
-# Use circular cursors to select regions of interest.
+# Use circular cursors in the phasor space to segment the images:
 
 signal = tifffile.imread(fetch('paramecium.lsm'))
 mean, real, imag = phasor_from_signal(signal, axis=0)
 
-label = label_from_phasor_circular(
-    real,
-    imag,
-    numpy.array(
-        [[-0.48, -0.65], [-0.22, -0.75], [0.40, -0.80], [0.66, -0.68]]
-    ),
-    radius=[0.15, 0.15, 0.15, 0.15],
-)
+center = [(-0.48, -0.65), (-0.22, -0.75), (0.4, -0.8), (0.66, -0.68)]
+radius = [0.15, 0.15, 0.15, 0.15]
 
+label = label_from_phasor_circular(real, imag, center, radius)
 
 # %%
-# Circular cursors
-# ----------------
-#
+# Show the circular cursors in the phasor plot:
 
 mask = mean > 1
-real = real[mask]
-imag = imag[mask]
-
-import matplotlib.pyplot as plt
-
-
-def cart2pol(x, y):
-    rho = numpy.sqrt(x**2 + y**2)
-    phi = numpy.arctan2(y, x)
-    return (phi, rho)
-
-
-# components centers in polars
-t1, r1 = cart2pol(-0.48, -0.65)
-t2, r2 = cart2pol(-0.22, -0.75)
-t3, r3 = cart2pol(0.40, -0.80)
-t4, r4 = cart2pol(0.66, -0.68)
 
-plotcursors = True
-if plotcursors:
-    plot = PhasorPlot(allquadrants=True, title='Test cursors selection')
-    plot.polar_cursor(t1, r1, radius=0.15)
-    plot.polar_cursor(t2, r2, radius=0.15)
-    plot.polar_cursor(t3, r3, radius=0.15)
-    plot.polar_cursor(t4, r4, radius=0.15)
-    plot.hist2d(real, imag, cmap='Blues')
+plot = PhasorPlot(allquadrants=True, title='Circular cursors')
+plot.hist2d(real[mask], imag[mask])
+plot.cursor(*center[0], radius=radius[0], color='tab:orange', linestyle='-')
+plot.cursor(*center[1], radius=radius[1], color='tab:green', linestyle='-')
+plot.cursor(*center[2], radius=radius[2], color='tab:red', linestyle='-')
+plot.cursor(*center[3], radius=radius[3], color='tab:purple', linestyle='-')
 
-plt.figure()
-plt.imshow(label)
-plt.show()
+# %%
+# Show the label image:
 
+fig, ax = pyplot.subplots()
+ax.set_title('Labels from circular cursors')
+plt = ax.imshow(label, vmin=0, vmax=10, cmap='tab10')
+fig.colorbar(plt)
+pyplot.show()
 
 # %%
 # Range cursors
 # -------------
 #
-# Compute phasor from signal and get the phase values.
+# Create labels from ranges of phase values computed from phasor coordinates:
 
 mean, real, imag = phasor_from_signal(signal, axis=0)
 phase, _ = phasor_to_polar(real, imag)
-rang = numpy.array(
-    [(0, numpy.pi), (-numpy.pi / 2, 0), (-numpy.pi, -numpy.pi / 2)]
-)
-label = label_from_ranges(phase, ranges=rang)
 
+ranges = [(0, math.pi), (-math.pi / 2, 0), (-math.pi, -math.pi / 2)]
 
-plt.figure()
-plt.imshow(label)
+label = label_from_ranges(phase, ranges=ranges)
 
-plot = PhasorPlot(allquadrants=True, title='Raw phasor')
-plot.hist2d(real, imag, cmap='Blues')
+# %%
+# Show the label image:
+
+fig, ax = pyplot.subplots()
+ax.set_title('Labels from phase ranges')
+plt = ax.imshow(label, vmin=0, vmax=10, cmap='tab10')
+fig.colorbar(plt)
+pyplot.show()
 
-plt.show()
+# %%
+# Show the range cursors in the phasor plot:
+
+plot = PhasorPlot(allquadrants=True, title='Phase range cursors')
+plot.hist2d(real, imag, cmap='Blues')
+plot.polar_cursor(
+    phase=ranges[0][0],
+    phase_limit=ranges[0][1],
+    color='tab:orange',
+    linestyle='-',
+)
+plot.polar_cursor(
+    phase=ranges[1][0],
+    phase_limit=ranges[1][1],
+    color='tab:green',
+    linestyle='-',
+)
+plot.polar_cursor(
+    phase=ranges[2][0],
+    phase_limit=ranges[2][1],
+    color='tab:red',
+    linestyle='-',
+)
+plot.show()

schutyb · 2024-04-29T22:59:54Z

thnaks @cgohlke I´ll apply the changes tonight and have a look at numpy.digitize bc I didn´t do it. I update everything tommorrow during the day so we keep interating until it gets ready.

Also I didn´t try to optimize it or improve the functions bc you mention that eventually we could write them in cython. Do you think I should do it now?

…up (phasorpy#64)

schutyb · 2024-05-17T02:28:10Z

@cgohlke I changed the function label_from_ranges to label_from_lut so for any given lut that is created with some ranges that can overlap we can select ROI´s in the phasor. I add this in the tutorial with some plot using the polar cursors.

Please have a look when you can and give me your feedback.

cgohlke · 2024-05-17T03:32:23Z

src/phasorpy/cursors.py

+#############################################
+#############################################


cgohlke · 2024-05-17T03:34:23Z

src/phasorpy/cursors.py

+    min_vals1: NDArray,
+    max_vals1: NDArray,
+    min_vals2: NDArray,
+    max_vals2: NDArray,


Array inputs should be ArrayLike, not NDArray.

cgohlke · 2024-05-17T03:35:08Z

src/phasorpy/cursors.py

+    - min_vals1: NDArray
+        Array of minimum values to binarize data1.
+    - max_vals1: NDArray
+        Array of maximum values to binarize data1.
+    - min_vals2: NDArray
+        Array of minimum values to binarize data2.
+    - max_vals2: NDArray
+        Array of maximum values to binarize data2.


Follow numpy docstring standard.

cgohlke · 2024-05-17T03:35:20Z

src/phasorpy/cursors.py

+
+    Returns
+    -------
+    - dict


Follow numpy docstring standard.

cgohlke · 2024-05-17T03:36:37Z

src/phasorpy/cursors.py

+    max_vals2: NDArray,
+) -> dict:
+    """
+    Create a Lookup Table (LUT) with two pairs of minimum and maximum values.


-> """Return lookup table (LUT) with two pairs of minimum and maximum values.

cgohlke · 2024-05-17T03:40:48Z

src/phasorpy/cursors.py

+    - data1: NDArray
+        The first data array.
+    - data2: NDArray
+        The second data array.
+    - lut: dict
+        Lookup Table (LUT) mapping input values to binarized output values.
+
+    Returns
+    -------
+    - label: NDArray:
+        The binarized array.


Follow numpy docstring standard.

cgohlke · 2024-05-17T03:41:01Z

src/phasorpy/cursors.py

+    Raises
+    ------
+    ValueError
+        'Input arrays must have same shapes'


cgohlke · 2024-05-17T03:42:28Z

src/phasorpy/cursors.py

+#### EXAMPLES
+# Examples
+# --------
+# Create a LUT based on ranges values:
+
+# >>> create_lut(
+# ...     min_vals1 = numpy.array([0, 3, 6]),
+# ...     max_vals1 = numpy.array([2, 5, 8]),
+# ...     min_vals2 = numpy.array([1, 4, 7]),
+# ...     max_vals2 = numpy.array([3, 6, 9]))
+# {((0, 2), (1, 3)): 1, ((0, 2), (4, 6)): 2, ((0, 2), (7, 9)): 3,
+# ... ((3, 5), (1, 3)): 4, ((3, 5), (4, 6)): 5, ((3, 5), (7, 9)): 6,
+# ... ((6, 8), (1, 3)): 7, ((6, 8), (4, 6)): 8, ((6, 8), (7, 9)): 9}
+
+# Example
+# -------
+# >>> arr1 = numpy.array([[1.2, 2.4, 3.5], [4.7, 5.1, 6.9], [7.3, 8.6, 9.0]])
+# >>> arr2 = numpy.array([[0.8, 2.1, 3.9], [4.2, 5.7, 6.3],[7.5, 8.2, 9.5]])
+# >>> lut = {((0, 2), (1, 3)): 1, ((0, 2), (4, 6)): 2, ((0, 2), (7, 9)): 3,
+# ... ((3, 5), (1, 3)): 4, ((3, 5), (4, 6)): 5, ((3, 5), (7, 9)): 6,
+# ... ((6, 8), (1, 3)): 7, ((6, 8), (4, 6)): 8, ((6, 8), (7, 9)): 9}
+# >>> label = label_from_lut(arr1, arr2, lut)
+# array([[0, 0, 0], [5, 0, 0], [9, 0, 0]])


cgohlke · 2024-05-17T03:49:42Z

src/phasorpy/cursors.py

+    ------
+    ValueError
+        'Input arrays must have same shapes'
+


Example is missing.

cgohlke · 2024-05-17T03:49:57Z

src/phasorpy/cursors.py

+    ------
+    ValueError
+        'Input array must have same shapes'
+    """


Example is missing

cgohlke · 2024-05-17T04:11:25Z

This PR contains changes which do not belong here. Please update your branch from the main phasorpy branch as discussed before.

I find the use of create_lut and label_from_lut hard to follow, especially for overlapping bins. Can you document how the labels for overlapping bins are determined. It also seems to differ from label_from_phasor_circular, which does not handle overlaps? The implementation looks inefficient, especially for large number of bins. Maybe the non-overlapping case could be implemented/replaced with scipy.stats.binned_statistic_2d? Another option could be to replace the dict LUT with a 2D numpy array.

cgohlke · 2024-05-17T04:11:59Z

src/phasorpy/cursors.py

@@ -0,0 +1,216 @@
+""" Select phasor coordinates.
+
+    The ``phasorpy.cursors`` module provides functions to:


Remove indent.

Bruno Schüty and others added 7 commits March 15, 2024 12:20

circular cursos is ready

1d03909

Merge branch 'phasorpy:main' into cursors

6099633

compute the selection for circular & range cursors

17a515c

correct func names

a9f937a

add test file for cursors

9b3dd8e

add the test_cursors functions

386b293

passed

7e84202

schutyb assigned cgohlke, bruno-pannunzio, schutyb and lmalacrida Mar 26, 2024

schutyb added the enhancement New feature or request label Mar 26, 2024

schutyb added 3 commits March 26, 2024 19:58

change range_cursor(values, ranges) output

d6dbfdf

fix minor errors in the examples

45ee613

python -m black --check not pass yet

33a9e04

correct module introduction

947bae2

cgohlke unassigned cgohlke, bruno-pannunzio and lmalacrida Mar 27, 2024

cgohlke requested review from cgohlke, bruno-pannunzio and lmalacrida March 27, 2024 00:00

cgohlke changed the title ~~Cursors module~~ Add cursors module Mar 27, 2024

correct misspelled characters

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cgohlke reviewed Mar 27, 2024

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cgohlke mentioned this pull request Apr 29, 2024

WIP: Add LFD workshop FLIM tutorial #63

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schutyb added 2 commits April 29, 2024 11:52

two basic funtions for cursors

237ebb1

corrections with mypy

9371daf

Merge branch 'main' into cursors

8710897

schutyb added 7 commits April 30, 2024 10:38

Add Cgohlke changes, still need to add some more

7577bd3

changed label_from_ranges using digitize

341b0b7

then change range cursors for polar cursors

52ba934

add LUT based label funtion and tutorials

2ebbb9d

correct the mypy erros

6a7707b

mypy errors corrected

4c69cec

correct cursors.py for blak format

fd3968d

cgohlke mentioned this pull request May 9, 2024

Format docstring examples with blackdoc #66

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dependabot bot and others added 6 commits May 16, 2024 22:36

Bump peaceiris/actions-gh-pages from 3 to 4 in the github-actions gro…

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…up (phasorpy#64)

Format docstring examples with blackdoc (phasorpy#66)

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Add phasor_at_harmonic function (phasorpy#65)

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commit with no error in pytest

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Add cursors module #48

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		#############################################
		#############################################

		@@ -0,0 +1,216 @@
		""" Select phasor coordinates.

		The ``phasorpy.cursors`` module provides functions to:

Add cursors module #48

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schutyb commented Mar 26, 2024

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