Tidy up use of progress bar display markers.

* Move progressbar stuff to subroutine
* Rename pbar -> progress_bar
  Resist temptation towards short, meaningless variable names...
  even when they're just a progress bar object.

Author: timstaley

docs/source/notebooks/simulate_and_image.ipynb

@@ -162,15 +162,15 @@
    "source": [
     "kernel_support = 3\n",
     "kernel_func = GaussianSinc(trunc=kernel_support)\n",
-    "with Tqdm() as pbar:\n",
+    "with Tqdm() as progress_bar:\n",
     "    image, beam = imager.image_visibilities(data_vis, uvw_lambda,\n",
     "                                            image_size=image_size,\n",
     "                                            cell_size=cell_size,\n",
     "                                            kernel_func=kernel_func,\n",
     "                                            kernel_support=kernel_support,\n",
     "                                            kernel_exact=True,\n",
     "                                            kernel_oversampling=None,\n",
-    "                                            pbar=pbar\n",
+    "                                            progress_bar=progress_bar\n",
     "                                            )\n",
     "image = np.real(image)"
    ]
@@ -247,5 +247,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
-}
+ "nbformat_minor": 0
+}

setup.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env python
 
-import versioneer
 from setuptools import find_packages, setup
 
+import versioneer
+
 install_requires = [
     'astropy',
     'attrs>=16.3.0',

src/fastimgproto/fixtures/profiling.py

@@ -1,6 +1,5 @@
-from memory_profiler import profile
-
 from fastimgproto.sourcefind.image import SourceFindImage
+from memory_profiler import profile
 
 
 @profile

src/fastimgproto/gridder/gridder.py

@@ -7,17 +7,21 @@
 import tqdm
 
 from fastimgproto.gridder.kernel_generation import Kernel
+from fastimgproto.utils import reset_progress_bar
 
 logger = logging.getLogger(__name__)
 
 
-def convolve_to_grid(kernel_func, support,
+def convolve_to_grid(kernel_func,
+                     support,
                      image_size,
-                     uv, vis,
+                     uv,
+                     vis,
+                     vis_weights,
                      exact=True,
                      oversampling=0,
                      raise_bounds=True,
-                     pbar=None):
+                     progress_bar=None):
     """
     Grid visibilities, calculating the exact kernel distribution for each.
 
@@ -60,7 +64,7 @@ def convolve_to_grid(kernel_func, support,
             Larger values give a finer-sampled set of pre-cached kernels.
         raise_bounds (bool): Raise an exception if any of the UV
             samples lie outside (or too close to the edge) of the grid.
-        pbar (tqdm.tqdm): [Optional] progressbar to update.
+        progress_bar (tqdm.tqdm): [Optional] progressbar to update.
 
     Returns:
         tuple: (vis_grid, sampling_grid)
@@ -105,10 +109,9 @@ def convolve_to_grid(kernel_func, support,
         oversampled_offset = calculate_oversampled_kernel_indices(
             uv_frac, oversampling)
     logger.debug("Gridding {} visibilities".format(len(good_vis_idx)))
-    if pbar is not None:
-        pbar.total = len(good_vis_idx)
-        pbar.n = 0
-        pbar.set_description('Gridding visibilities')
+    if progress_bar is not None:
+        reset_progress_bar(progress_bar, len(good_vis_idx),
+                           'Gridding visibilities')
     for idx in good_vis_idx:
         gc_x, gc_y = kernel_centre_on_grid[idx]
         # Generate a convolution kernel with the precise offset required:

src/fastimgproto/imager.py

@@ -14,7 +14,7 @@ def image_visibilities(vis, uvw_lambda,
                        kernel_exact=True,
                        kernel_oversampling=0,
                        normalize=True,
-                       pbar=None):
+                       progress_bar=None):
     """
     Args:
         vis (numpy.ndarray): Complex visibilities.
@@ -49,7 +49,7 @@ def image_visibilities(vis, uvw_lambda,
             should be normalized such that the beam peaks at a value of
             1.0 Jansky. You normally want this to be true, but it may be
             interesting to check the raw values for debugging purposes.
-        pbar (tqdm.tqdm): [Optional] progressbar to update.
+        progress_bar (tqdm.tqdm): [Optional] progressbar to update.
 
     Returns:
         tuple: (image, beam)
@@ -76,7 +76,7 @@ def image_visibilities(vis, uvw_lambda,
                                              vis=vis,
                                              exact=kernel_exact,
                                              oversampling=kernel_oversampling,
-                                             pbar=pbar
+                                             progress_bar=progress_bar
                                              )
     image = fft_to_image_plane(vis_grid)
     beam = fft_to_image_plane(sample_grid)

src/fastimgproto/scripts/image.py

@@ -44,15 +44,16 @@ def cli(config_json, in_vis, out_img):
     kernel_support = 3
     kernel_func = GaussianSinc(trunc=kernel_support)
 
-    with Tqdm() as pbar:
-        image, beam = imager.image_visibilities(vis, uvw_lambda,
+    with Tqdm() as progress_bar:
+        image, beam = imager.image_visibilities(vis,
+                                                uvw_lambda=uvw_lambda,
                                                 image_size=image_size,
                                                 cell_size=cell_size,
                                                 kernel_func=kernel_func,
                                                 kernel_support=kernel_support,
                                                 kernel_exact=True,
                                                 kernel_oversampling=None,
-                                                pbar=pbar
+                                                progress_bar=progress_bar
                                                 )
 
     np.savez(out_img, image=image, beam=beam)

src/fastimgproto/scripts/reduce.py

@@ -114,14 +114,15 @@ def main(uvw_lambda,
     kernel_support = 3
     kernel_func = GaussianSinc(trunc=kernel_support)
     logger.info("Imaging residual visibilities")
-    with Tqdm() as pbar:
-        image, beam = imager.image_visibilities(residual_vis, uvw_lambda,
+    with Tqdm() as progress_bar:
+        image, beam = imager.image_visibilities(residual_vis,
+                                                uvw_lambda=uvw_lambda,
                                                 image_size=image_size,
                                                 cell_size=cell_size,
                                                 kernel_func=kernel_func,
                                                 kernel_support=kernel_support,
                                                 kernel_exact=True,
-                                                pbar=pbar)
+                                                progress_bar=progress_bar)
     logger.info("Running sourcefinder on image")
     sfimage = SourceFindImage(data=np.real(image),
                               detection_n_sigma=detection_n_sigma,

src/fastimgproto/scripts/simulate_data.py

@@ -42,10 +42,10 @@ def cli(output_npz, nstep):
                                           start_time=Time('2017-01-01'))
     obs_times = transit_time + np.linspace(-1, 1, nstep) * u.hr
     logger.info("Generating UVW-baselines for {} timesteps".format(nstep))
-    with Tqdm() as pbar:
+    with Tqdm() as progress_bar:
         uvw_m = telescope.uvw_tracking_skycoord(
             pointing_centre, obs_times,
-            pbar=pbar
+            progress_bar=progress_bar
         )
     # From here on we use UVW as multiples of wavelength, lambda:
     uvw_lambda = (uvw_m / wavelength).to(u.dimensionless_unscaled).value

src/fastimgproto/telescope/base.py

@@ -16,6 +16,7 @@
     xyz_to_uvw_rotation_matrix,
     z_rotation_matrix,
 )
+from fastimgproto.utils import reset_progress_bar
 
 _validator_optional_ndarray = attr.validators.optional(
     attr.validators.instance_of(np.ndarray))
@@ -208,7 +209,7 @@ def _uvw_tracking_skycoord_by_lha(self, pointing_centre, obs_times,
         return lha_uvw_map
 
     def uvw_tracking_skycoord(self, pointing_centre, obs_times,
-                              pbar=None):
+                              progress_bar=None):
         """
         Calculate the UVW-array towards pointing centre for all obs_times.
 
@@ -222,25 +223,24 @@ def uvw_tracking_skycoord(self, pointing_centre, obs_times,
                 for UVW calculation.
             obs_times (list): List of :class:`astropy.time.Time`, the instants
                 of observation.
-            pbar (tqdm.tqdm): [Optional] progressbar to update.
+            progress_bar (tqdm.tqdm): [Optional] progressbar to update.
         Returns:
             astropy.units.Quantity: UVW-array, with units of metres.
         """
         n_baselines = len(self.baseline_local_xyz)
         uvw_array = np.zeros((len(obs_times) * n_baselines, 3),
                              dtype=np.float_) * self.baseline_local_xyz.unit
-        if pbar is not None:
-            pbar.total=len(obs_times)
-            pbar.desc = 'Generating UVW-baselines'
+        if progress_bar is not None:
+            reset_progress_bar(progress_bar, len(obs_times), 'Generating UVW-baselines')
 
         for idx, time in enumerate(obs_times):
             lha = self.lha(pointing_centre.ra, time)
             output_slice = slice(idx * n_baselines, (idx + 1) * n_baselines)
             uvw_array[output_slice] = self.uvw_at_local_hour_angle(
                 local_hour_angle=lha, dec=pointing_centre.dec
             )
-            if pbar is not None:
-                pbar.update()
+            if progress_bar is not None:
+                progress_bar.update()
         return uvw_array
 
 

src/fastimgproto/utils.py

@@ -0,0 +1,26 @@
+
+
+def reset_progress_bar(progress_bar, total, description="Doing something"):
+    """
+    Short subroutine to reset a progress bar.
+
+    Currently setup for tqdm progress bars, but we could imagine this
+    function evolving for a different libary or even handling progress bars
+    polymorphically.
+
+    Mainly it just tidies 3 irrelevant lines into one clear function call,
+    which is less distracting from key logic.
+
+    Currently
+    Args:
+        progress_bar (tqdm.tqdm): Progress display class
+        total (int): total number of iterations being stepped through
+        description (str):  Description to display
+
+    Returns:
+
+    """
+    progress_bar.n = 0
+    progress_bar.total=total
+    progress_bar.desc=description
+    return