Update get_rfi_mask to work with Python 3.11

.gitignore

@@ -9,6 +9,7 @@
 dist
 build
 eggs
+.eggs
 parts
 bin
 var
@@ -28,6 +29,7 @@ pip-log.txt
 nosetests.xml
 *junit-*
 htmlcov
+.pytest_cache
 
 # Translations
 *.mo
@@ -42,4 +44,11 @@ output/*.html
 output/*/index.html
 
 # Sphinx
-docs/_build
+docs/_build
+
+# Virtual environments
+.virt
+virt
+
+# Media
+img

README.rst

@@ -1,6 +1,6 @@
-=============================
+====================================================
 SEEK: Signal Extraction and Emission Kartographer
-=============================
+====================================================
 
 .. image:: https://travis-ci.org/cosmo-ethz/seek.png?branch=master
         :target: https://travis-ci.org/cosmo-ethz/seek

docs/conf.py

@@ -129,7 +129,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.

docs/mitigation.rst

@@ -3,7 +3,7 @@ RFI mitigation
 ================
 
 SEEK's RFI mitigation follows the `Offringa et al. <http://arxiv.org/pdf/1002.1957v1.pdf>`_ `SumThreshold` algorithm. 
-It's implemented in pure Python and JIT-compiled for speed with the `HOPE <https://github.com/cosmo-ethz/hope>`_ package.
+It's implemented in pure Python. It is no longer JIT-compiled with the `HOPE <https://github.com/cosmo-ethz/hope>`_ package as `HOPE` is now deprecated.
 
 It can easily be used without of the SEEK data processing pipeline::
 

docs/seek.rst

@@ -1,23 +1,23 @@
-seek Package
+seek package
 ============
 
-:mod:`seek` Package
--------------------
-
-.. automodule:: seek.__init__
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 Subpackages
 -----------
 
 .. toctree::
+   :maxdepth: 4
+
+   seek.calibration
+   seek.config
+   seek.mapmaking
+   seek.mitigation
+   seek.plugins
+   seek.utils
 
-    seek.calibration
-    seek.config
-    seek.mapmaking
-    seek.mitigation
-    seek.plugins
-    seek.utils
+Module contents
+---------------
 
+.. automodule:: seek
+   :members:
+   :undoc-members:
+   :show-inheritance:

example_rfi.py

@@ -0,0 +1,27 @@
+import cv2 as cv
+import numpy.ma as ma
+
+from seek.mitigation import sum_threshold
+
+try:
+    spec = cv.imread("img/spec.png", cv.IMREAD_GRAYSCALE)
+    if spec is None:
+        raise FileNotFoundError()
+except:
+    print("File not found. Try again.")
+    exit()
+
+spec_masked = ma.array(spec, mask=ma.nomask)
+
+rfi_mask = sum_threshold.get_rfi_mask(
+    tod=spec_masked, 
+    mask=None,
+    chi_1=35000,
+    eta_i=[0.5],
+    #eta_i=[0.5, 0.55, 0.62, 0.75, 1],
+    normalize_standing_waves=True,
+    suppress_dilation=False,
+    plotting=True,
+    sm_kwargs=None,
+    di_kwargs=None
+)

requirements-rfi.txt

@@ -0,0 +1,12 @@
+# Requirements for the `seek.mitigation.get_rfi_mask` function
+numpy==2.0.1
+scipy==1.14.0
+
+# Requirements to run the example_rfi.py file
+opencv-python==4.10.0.84
+matplotlib==3.9.1
+
+# Requirements to successfully run the Makefile options
+flake8
+pytest
+sphinx

requirements.readthedocs.txt

@@ -3,7 +3,6 @@ scipy
 Cython
 h5py
 mock
-hope
 pyephem
 six
 astropy

requirements.txt

@@ -3,7 +3,6 @@ scipy
 Cython
 h5py
 mock
-hope
 pyephem
 six
 healpy

seek/calibration/fitting.py

@@ -22,9 +22,7 @@
 
 import numpy as np
 from scipy.optimize import curve_fit
-import hope
 
-@hope.jit
 def gauss(x, a, x0, sigma, b, c):
     """
     Gaussian model plus a linear background.

seek/mitigation/sum_threshold.py

@@ -17,13 +17,14 @@
 
 author: jakeret
 '''
+
 from __future__ import print_function, division, absolute_import, unicode_literals
 
+import warnings
+
 import numpy as np
 from scipy import ndimage
 
-import hope
-
 from seek.mitigation import sum_threshold_utils
 from seek.utils.tod_utils import get_empty_mask
 from seek.utils import filter
@@ -41,7 +42,6 @@
 STRUCT_SIZE = 3
 
 
-@hope.jit
 def _sumthreshold(data, mask, i, chi, ds0, ds1):
     """
     The operation of summing and thresholding.
@@ -111,7 +111,7 @@ def _run_sumthreshold(data, init_mask, eta, M, chi_i, sm_kwargs, plotting=True):
             st_mask = _sumthreshold(res.T, st_mask.T, m, chi, *res.T.shape).T
 
     if plotting:
-        sum_threshold_utils.plot_steps(data, st_mask, smoothed_data, res, "%s (%s)"%(eta, chi_i))
+        sum_threshold_utils.plot_steps(data, st_mask, smoothed_data, res, f"{eta} ({chi_i})")
 
     return st_mask
 
@@ -125,7 +125,7 @@ def binary_mask_dilation(mask, struct_size_0, struct_size_1):
 
     :return: dilated mask
     """
-    struct = np.ones((struct_size_0, struct_size_1), np.bool)
+    struct = np.ones((struct_size_0, struct_size_1), np.bool_)
     return ndimage.binary_dilation(mask, structure=struct, iterations=2)
 
 
@@ -159,19 +159,26 @@ def get_rfi_mask(tod, mask=None, chi_1=35000, eta_i=[0.5, 0.55, 0.62, 0.75, 1],
 
     :return mask: the mask covering the identified RFI
     """
+    if mask is None and not suppress_dilation:
+        warnings.warn("mask=None and suppress_dilation=False: Dilation will not be performed on an empty mask.", UserWarning)
+        suppress_dilation = True
+
     data = tod.data
 
     if mask is None:
         mask = get_empty_mask(data.shape)
 
-    if sm_kwargs is None: sm_kwargs = get_sm_kwargs()
+    if sm_kwargs is None:
+        sm_kwargs = get_sm_kwargs()
 
-    if plotting: sum_threshold_utils.plot_moments(data)
+    if plotting:
+        sum_threshold_utils.plot_moments(data, "Time and Frequency Statistics")
 
     if normalize_standing_waves:
         data = normalize(data, mask)
-
-        if plotting: sum_threshold_utils.plot_moments(data)
+        if plotting: 
+            title = "Time and Frequency Statistics After Normalizing Standing Waves"
+            sum_threshold_utils.plot_moments(data, title)
 
     p = 1.5
     m = np.arange(1, MAX_PIXELS)
@@ -184,13 +191,15 @@ def get_rfi_mask(tod, mask=None, chi_1=35000, eta_i=[0.5, 0.55, 0.62, 0.75, 1],
 
     dilated_mask = st_mask
     if not suppress_dilation:
-        if di_kwargs is None: di_kwargs = get_di_kwrags()
+        if di_kwargs is None:
+            di_kwargs = get_di_kwargs()
 
-        dilated_mask = binary_mask_dilation(dilated_mask - mask, **di_kwargs)
+        dilated_mask = binary_mask_dilation(np.logical_xor(dilated_mask, mask), **di_kwargs)
 
-        if plotting: sum_threshold_utils.plot_dilation(st_mask, mask, dilated_mask)
+        if plotting:
+            sum_threshold_utils.plot_dilation(st_mask, mask, dilated_mask)
 
-    return dilated_mask+mask
+    return dilated_mask + mask
 
 def get_sm_kwargs(kernel_m=KERNEL_M, kernel_n=KERNEL_N, sigma_m=SIGMA_M, sigma_n=SIGMA_N):
     """
@@ -205,7 +214,7 @@ def get_sm_kwargs(kernel_m=KERNEL_M, kernel_n=KERNEL_N, sigma_m=SIGMA_M, sigma_n
     """
     return dict(M=kernel_m, N=kernel_n, sigma_m=sigma_m, sigma_n=sigma_n)
 
-def get_di_kwrags(struct_size_0=STRUCT_SIZE, struct_size_1=STRUCT_SIZE):
+def get_di_kwargs(struct_size_0=STRUCT_SIZE, struct_size_1=STRUCT_SIZE):
     """
     Creates a dict with the dilation keywords.
 
@@ -229,7 +238,7 @@ def get_sumthreshold_kwargs(params):
                               params.sm_sigma_m,
                               params.sm_sigma_n,)
 
-    di_kwargs = get_di_kwrags(params.struct_size_0, params.struct_size_1)
+    di_kwargs = get_di_kwargs(params.struct_size_0, params.struct_size_1)
 
     return sm_kwargs, di_kwargs