start renaming pfb-clean -> pfb-imaging

Author: landmanbester

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: pfb-clean Workflow
+name: pfb-imaging Workflow
 
 on:
   push:
@@ -31,7 +31,7 @@ jobs:
       # - name: Pin setuptools
       #   run: python -m pip install setuptools==65.5
 
-      - name: Install pfb-clean
+      - name: Install pfb-imaging
         run: python -m pip install .[testing]
 
       - name: Run tests

Dockerfile

@@ -12,6 +12,6 @@ RUN apt -y update && \
 
 
 RUN python -m pip install -U pip setuptools wheel && \
-    python -m pip install -U pfb-clean@git+https://github.com/ratt-ru/pfb-clean@main && \
+    python -m pip install -U pfb-imaging@git+https://github.com/ratt-ru/pfb-imaging@main && \
     python -m pip install numpy==1.22 && \
     python -m pip cache purge

README.rst

@@ -1,10 +1,10 @@
-pfb-clean
+pfb-imaging
 =========
-Preconditioned forward-backward clean algorithm.
+Radio interferometric imaging suite base on the pre-conditioned forward-backward algorithm.
 
 Install the package by cloning and running
 
-:code:`$ pip install -e pfb-clean/`
+:code:`$ pip install -e pfb-imaging/`
 
 Note casacore needs to be installed on the system for this to work.
 
@@ -19,14 +19,6 @@ no binary mode eg
 
 :code:`$ pip install -e ducc`
 
-You may also have to make numba aware of the tbb layer by doing
-
-:code:`$ pip install tbb`
-
-:code:`$ export LD_LIBRARY_PATH=/path/to/venv/lib`
-
-see eg. https://github.com/ratt-ru/QuartiCal/issues/268
-
 If you find any of this useful please cite (for now)
 
 https://arxiv.org/abs/2101.08072

pfb/utils/fits.py

@@ -68,7 +68,7 @@ def set_wcs(cell_x, cell_y, nx, ny, radec, freq,
 
     header = w.to_header()
     header['RESTFRQ'] = fmean
-    header['ORIGIN'] = 'pfb-clean'
+    header['ORIGIN'] = 'pfb-imaging'
     header['BTYPE'] = 'Intensity'
     header['BUNIT'] = unit
     header['SPECSYS'] = 'TOPOCENT'

pfb/utils/misc.py

@@ -1444,52 +1444,52 @@ def combine_columns(x, y, dc, dc1, dc2):
     return x
 
 
-# def fft_interp(image, cellxi, cellyi, nxo, nyo,
-#                cellxo, cellyo, shiftx, shifty):
-#     '''
-#     Use non-uniform fft to interpolate image in a flux conservative way
-
-#     image   - input image
-#     cellxi  - input x cell-size
-#     cellyi  - input y cell-size
-#     nxo     - number of x pixels in output
-#     nyo     - number of y pixels in output
-#     cellxo  - output x cell size
-#     cellyo  - output y cell size
-#     shiftx  - shift x coordinate by this amount
-#     shifty  - shift y coordinate by this amount
-
-#     All sizes are assumed to be in radians.
-#         '''
-#     import matplotlib.pyplot as plt
-#     from scipy.fft import fftn, ifftn
-#     Fs = np.fft.fftshift
-#     iFs = np.fft.ifftshift
-#     # basic
-#     nx, ny = image.shape
-#     imhat = Fs(fftn(image))
-
-#     imabs = np.abs(imhat)
-#     imphase = np.angle(imhat) - 1.0
-#     # imphase = np.roll(imphase, nx//2, axis=0)
-#     imshift = ifftn(iFs(imabs*np.exp(1j*imphase))).real
-
-#     impad = np.pad(imhat, ((nx//2, nx//2), (ny//2, ny//2)), mode='constant')
-#     imo = ifftn(iFs(impad)).real
-
-#     print(np.sum(image) - np.sum(imo))
-
-#     plt.figure(1)
-#     plt.imshow(image/image.max(), vmin=0, vmax=1, interpolation=None)
-#     plt.colorbar()
-#     plt.figure(2)
-#     plt.imshow(imo/imo.max(), vmin=0, vmax=1, interpolation=None)
-#     plt.colorbar()
-#     plt.figure(3)
-#     plt.imshow(imshift/imshift.max() - image/image.max(), vmin=0, vmax=1, interpolation=None)
-#     plt.colorbar()
-
-#     plt.show()
+def fft_interp(image, cellxi, cellyi, nxo, nyo,
+               cellxo, cellyo, shiftx, shifty):
+    '''
+    Use non-uniform fft to interpolate image in a flux conservative way
+
+    image   - input image
+    cellxi  - input x cell-size
+    cellyi  - input y cell-size
+    nxo     - number of x pixels in output
+    nyo     - number of y pixels in output
+    cellxo  - output x cell size
+    cellyo  - output y cell size
+    shiftx  - shift x coordinate by this amount
+    shifty  - shift y coordinate by this amount
+
+    All sizes are assumed to be in radians.
+    '''
+import matplotlib.pyplot as plt
+from scipy.fft import fftn, ifftn
+Fs = np.fft.fftshift
+iFs = np.fft.ifftshift
+# basic
+nx, ny = image.shape
+imhat = Fs(fftn(image))
+
+# imabs = np.abs(imhat)
+# imphase = np.angle(imhat) - 1.0
+# imphase = np.roll(imphase, nx//2, axis=0)
+# imshift = ifftn(iFs(imabs*np.exp(1j*imphase))).real
+
+impad = np.pad(imhat, ((nx//2, nx//2), (ny//2, ny//2)), mode='constant')
+imo = ifftn(iFs(impad)).real
+
+print(np.sum(image) - np.sum(imo))
+
+plt.figure(1)
+plt.imshow(image/image.max(), vmin=0, vmax=1, interpolation=None)
+plt.colorbar()
+plt.figure(2)
+plt.imshow(imo/imo.max(), vmin=0, vmax=1, interpolation=None)
+plt.colorbar()
+# plt.figure(3)
+# plt.imshow(imshift/imshift.max() - image/image.max(), vmin=0, vmax=1, interpolation=None)
+# plt.colorbar()
+
+plt.show()
 
     # # coordinates on input grid
     # nx, ny = image.shapeimhat

pfb/workers/main.py

@@ -7,7 +7,6 @@ def cli():
     pass
 
 
-from pfb.workers import (init, grid, degrid,
-                         klean, restore, fwdbwd,
-                         spotless, model2comps,
+from pfb.workers import (init, grid, degrid, klean,
+                         restore, spotless, model2comps,
                          fluxmop, fastim, smoovie)

setup.py

@@ -28,14 +28,14 @@
 
 
 setup(
-     name='pfb-clean',
+     name='pfb-imaging',
      version=pfb.__version__,
      author="Landman Bester",
      author_email="lbester@sarao.ac.za",
-     description="Pre-conditioned forward-backward CLEAN algorithm",
+     description="Radio interferometric imaging suite base on the pre-conditioned forward-backward algorithm",
      long_description=long_description,
      long_description_content_type="text/markdown",
-     url="https://github.com/ratt-ru/pfb-clean",
+     url="https://github.com/ratt-ru/pfb-imaging",
      packages=find_packages(),
      include_package_data=True,
      zip_safe=False,

tbump.toml

@@ -1,5 +1,5 @@
 # Uncomment this if your project is hosted on GitHub:
-github_url = "https://github.com/ratt-ru/pfb-clean/"
+github_url = "https://github.com/ratt-ru/pfb-imaging/"
 
 [version]
 current = "0.0.1"