Merge changes from jwst-kpi xara version

.gitignore

@@ -1,14 +1,148 @@
-# compiled python modules
-*.pyc
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-# emacs temporary save files
-*~
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
 
-# setuptools distribution folder
-/dist/
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
 
-# python egg metadata, regenerated from source files by setuptools
-/*.egg-info
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
 
-# build folder
-/build/
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# emacs temporary save files
+*~

pyproject.toml

@@ -0,0 +1,2 @@
+[tool.pyright]
+typeCheckingMode = "off"

xara/core.py

@@ -480,13 +480,13 @@ def find_fourier_origin(img, mykpo, m2pix, bmax=6.0):
 
     # Find Fourier plane coordinates which will be considered for the re-centering
     uv_dist = np.sqrt(mykpo.kpi.UVC[:, 0]**2+mykpo.kpi.UVC[:, 1]**2)
-    uv_cutoff = np.where(uv_dist < float(r_cutoff))[0]
+    uv_cutoff = np.where(uv_dist < float(bmax))[0]
 
     # Find best sub-pixel shift
     img_fft = np.fft.rfft2(img_cent)
     best_xy_shift = leastsq(func=fourier_phase_resid_2d,
                             x0=np.array([0., 0.]),
-                            args=(img_fft, m2pix, uv, uv_cutoff),
+                            args=(img_fft, mykpo, m2pix, uv, uv_cutoff),
                             ftol=1E-1)[0]
 
     # Return best shift
@@ -514,7 +514,8 @@ def fourier_phase_resid_2d(xy, img_fft, mykpo, m2pix, uv, uv_cutoff):
 
 
 # =========================================================================
-def determine_origin(img, mask=None, algo="BCEN", verbose=True, wmin=10.0):
+def determine_origin(img, mask=None, algo="BCEN", verbose=True, wmin=10.0,
+                     mykpo=None, m2pix=None, bmax=None):
     ''' ------------------------------------------------------------
     Determines the origin of the image, using among possible algorithms.
 
@@ -540,6 +541,11 @@ def determine_origin(img, mask=None, algo="BCEN", verbose=True, wmin=10.0):
     if "cog" in algo.lower():
         (x0, y0) = centroid(img1, verbose)
 
+    elif "fpnm" in algo.lower():
+        if mykpo is None or m2pix is None or bmax is None:
+            raise ValueError("Need mykpo, m2pix, and bmax parameters")
+        (x0, y0) = find_fourier_origin(img1, mykpo, m2pix, bmax)
+
     else:
         (x0, y0) = find_psf_center(img1, verbose, nbit=10, wmin=wmin)
 
@@ -548,7 +554,8 @@ def determine_origin(img, mask=None, algo="BCEN", verbose=True, wmin=10.0):
 
 # =========================================================================
 def recenter(im0, mask=None, algo="BCEN", subpix=True, between=False,
-             verbose=True):
+             verbose=True, return_center=False, dxdy=None, mykpo=None,
+             m2pix=None, bmax=None):
     ''' ------------------------------------------------------------
     Re-centering algorithm of a 2D image im0 for kernel-analysis
 
@@ -563,6 +570,18 @@ def recenter(im0, mask=None, algo="BCEN", subpix=True, between=False,
     - subpix: sub-pixel recentering         (boolean, default=True)
     - between: center in between 4 pixels   (boolean, default=False)
     - verbose: display some additional info (boolean, default=True)
+    - return_center: return center coordinate in original image (boolean, default=False)
+    - dxdy: center coordinates to use, origin is found with `algo` if None (Tuple[float], default=None)
+    - mykpo: KPO object, used to determine origin with FPNM (xara.kpo.KPO, default=None)
+    - m2pix: Meter to pixel scaling parameter for FPNM (float, default=None)
+    - bmax: Max baseline (in m) for FPNM (float, default=None)
+
+    Returns:
+    -------
+    - img: The recentered image
+    - If `return_center` is True:
+      + dx_temp: x coordinate of the center in original image
+      + dy_temp: y coordinate of the center in original image
 
     Remarks:
     -------
@@ -572,18 +591,25 @@ def recenter(im0, mask=None, algo="BCEN", subpix=True, between=False,
 
     ysz, xsz = im0.shape
 
-    (x0, y0) = determine_origin(im0, mask=mask, algo=algo, verbose=verbose)
+    if dxdy is None:
+        (x0, y0) = determine_origin(im0, mask=mask, algo=algo, verbose=verbose,
+                                    mykpo=mykpo, m2pix=m2pix, bmax=bmax)
 
-    dy, dx = (y0-ysz/2), (x0-xsz/2)
-    if between:
-        dy += 0.5
-        dx += 0.5
+        dy, dx = (y0-ysz/2), (x0-xsz/2)
+        if between:
+            dy += 0.5
+            dx += 0.5
 
-    if verbose:
-        print("centroid: dx=%+5.2f, dy=%+5.2f\n" % (dx, dy),
-              end="", flush=True)
+        if verbose:
+            print("centroid: dx=%+5.2f, dy=%+5.2f\n" % (dx, dy),
+                  end="", flush=True)
+
+    else:
+        dx, dy = dxdy
 
     # integer pixel recentering first
+    dx_temp = dx
+    dy_temp = dy
     im0 = np.roll(np.roll(im0, -int(round(dx)), axis=1),
                   -int(round(dy)), axis=0)
 
@@ -619,7 +645,10 @@ def recenter(im0, mask=None, algo="BCEN", subpix=True, between=False,
         offset = np.exp(1j*slope)
         dummy = np.real(shift(ifft(offset * fft(shift(im)))))
         im0 = dummy[oriy:oriy+ysz, orix:orix+xsz]
-    return im0
+    if not return_center:
+        return im0
+    else:
+        return im0, dx_temp, dy_temp
 
 
 # =========================================================================
@@ -780,6 +809,63 @@ def uv_phase_regrid_matrix(UVD, UVS, rad):
     return GG
 
 
+def hexagon(dim, width, interp_edge=True):
+    """This function creates a hexagon.
+
+    Adapted from: https://github.com/mikeireland/opticstools/blob/master/opticstools/utils.py#L164
+    by Mike Ireland under MIT License
+
+    Parameters
+    ----------
+    dim: int
+        Size of the 2D array
+    width: int
+        flat-to-flat width of the hexagon
+
+    Returns
+    -------
+    pupil: float array (sz,sz)
+        2D array hexagonal pupil mask
+    """
+    x = np.arange(dim) - dim / 2.0
+    xy = np.meshgrid(x, x)
+    xx = xy[1]
+    yy = xy[0]
+    hex = np.zeros((dim, dim))
+    scale = 1.5
+    offset = 0.5
+    if interp_edge:
+        # !!! Not fully implemented yet. Need to compute the orthogonal distance
+        # from each line and accurately find fractional area of each pixel.
+        hex = (
+            np.minimum(np.maximum(width / 2 - yy + offset, 0), 1)
+            * np.minimum(np.maximum(width / 2 + yy + offset, 0), 1)
+            * np.minimum(
+                np.maximum((width - np.sqrt(3) * xx - yy + offset) * scale, 0), 1
+            )
+            * np.minimum(
+                np.maximum((width - np.sqrt(3) * xx + yy + offset) * scale, 0), 1
+            )
+            * np.minimum(
+                np.maximum((width + np.sqrt(3) * xx - yy + offset) * scale, 0), 1
+            )
+            * np.minimum(
+                np.maximum((width + np.sqrt(3) * xx + yy + offset) * scale, 0), 1
+            )
+        )
+    else:
+        w = np.where(
+            (yy < width / 2)
+            * (yy > (-width / 2))
+            * (yy < (width - np.sqrt(3) * xx))
+            * (yy > (-width + np.sqrt(3) * xx))
+            * (yy < (width + np.sqrt(3) * xx))
+            * (yy > (-width - np.sqrt(3) * xx))
+        )
+        hex[w] = 1.0
+    return hex
+
+
 # =========================================================================
 def create_discrete_model(apert, ppscale, step, binary=True, tmin=0.8):
     '''------------------------------------------------------------------