Merge pull request #433 from GreenBankObservatory/issue_336

Issue 336

docs/source/_static/css/custom.css

@@ -10,6 +10,20 @@ are more visible */
   background-color: #C6B9D2;
 }
 
+/*
+ * */
+.widget-subarea {
+    background-color: var(--pst-color-surface) !important;
+    border-radius: 0.25rem !important;
+    /*border: 1px solid var(--mystnb-stdout-border-color) !important;*/
+    /*background: var(--mystnb-stdout-bg-color) !important;*/
+}
+
+div.output.text_html {
+    background-color: var(--pst-color-background) !important;
+    background: var(--pst-color-background) !important;
+}
+
 .black {
     color: black;
 }

docs/source/conf.py

@@ -59,6 +59,7 @@
     "numpydoc",
     "sphinx_inline_tabs",
     "sphinx_design",
+    "sphinx_copybutton",
 ]
 
 numpydoc_show_class_members = True
@@ -263,6 +264,8 @@
 
 # Cache notebooks to only re-run when cells change
 nb_execution_mode = "cache"
+# Use this mode if working on the documentation with sphinx-autobuild.
+# nb_execution_mode = "auto"
 
 # Where to store the notebook cache
 nb_execution_cache_path = "jupyter_cache"
@@ -273,3 +276,7 @@
     "dollarmath",
 ]
 myst_dmath_double_inline = True
+
+
+# -- sphinx-copybutton config -------------------------------------
+copybutton_exclude = ".linenos, .gp"

notebooks/examples/dataIO.ipynb

@@ -757,7 +757,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.0"
+   "version": "3.10.0"
   }
  },
  "nbformat": 4,

notebooks/examples/flagging.ipynb

@@ -320,7 +320,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.image.AxesImage at 0x7a1f64721dd0>"
+       "<matplotlib.image.AxesImage at 0x7f146739bdc0>"
       ]
      },
      "execution_count": 8,
@@ -459,10 +459,40 @@
     "ps.plot(xaxis_unit=\"chan\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "2debf76f-0a0d-4062-b23d-00c02d4ada5c",
+   "metadata": {},
+   "source": [
+    "## Removing Flags\n",
+    "\n",
+    "To remove flags from the `GBTFITSLoad` object use the `clear_flags` method."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "6a96b98e-8bd9-4959-a190-800ad10d6c4d",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " ID TAG OBJECT BANDWID DATE-OBS DURATION EXPOSURE TSYS TDIM7 TUNIT7 CTYPE1 CRVAL1 CRPIX1 CDELT1 CTYPE2 ... PLNUM FDNUM INT INTNUM NSAVE HDU BINTABLE ROW PROC OBSTYPE SUBOBSMODE FITSINDEX CHAN UTC # SELECTED\n",
+      "--- --- ------ ------- -------- -------- -------- ---- ----- ------ ------ ------ ------ ------ ------ ... ----- ----- --- ------ ----- --- -------- --- ---- ------- ---------- --------- ---- --- ----------\n"
+     ]
+    }
+   ],
+   "source": [
+    "sdfits.clear_flags()\n",
+    "sdfits.flags.show()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b00993ae-a385-4293-9182-f34bd18432b3",
+   "id": "4bb26ea3-602a-4e72-96df-87235c29105c",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -484,7 +514,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.10.0"
   }
  },
  "nbformat": 4,

notebooks/examples/frequencyswitch.ipynb

@@ -6,7 +6,6 @@
    "metadata": {},
    "source": [
     "# Frequency-switched Data Reduction\n",
-    "-----------------------------------\n",
     "\n",
     "This notebook shows how to use `dysh` to calibrate a frequency switched observations. The idea is similar to an OnOff observation, except the telescope does not move to an Off in position on the sky, but moves its intermediate frequency in frequency space. Here we call the On and Off the Sig and Ref, but both will have the signal, just shifted in the band. Since the telescope is always tracking the target, combining the Sig and a shifted (folded) Ref, a $\\sqrt{2}$ improvement in signal-to-noise can be achieved.\n",
     "\n",
@@ -724,7 +723,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.0"
+   "version": "3.10.0"
   },
   "toc": {
    "base_numbering": 0

notebooks/examples/nodding.ipynb

@@ -6,7 +6,6 @@
    "metadata": {},
    "source": [
     "# Nodding Data Reduction\n",
-    "------------------------\n",
     "\n",
     "This notebook shows the reduction path of a nodding observation in a multi-beam receiver.\n",
     "\n",
@@ -558,7 +557,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.4"
+   "version": "3.10.0"
   }
  },
  "nbformat": 4,

notebooks/examples/positionswitch.ipynb

@@ -6,7 +6,6 @@
    "metadata": {},
    "source": [
     "# Position-Switched Data Reduction\n",
-    "----------------------------------\n",
     "\n",
     "This notebook shows how to use `dysh` to calibrate an OnOff observation.\n",
     "It retrieves and calibrates position-switch scans using `GBTFITSLoad.getps()`, which returns a `ScanBlock` object.  OffOn observations can be reduced the same way."
@@ -929,7 +928,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.0"
+   "version": "3.10.0"
   },
   "toc": {
    "base_numbering": 0

notebooks/examples/smoothing.ipynb

@@ -6,7 +6,6 @@
    "metadata": {},
    "source": [
     "# Smoothing\n",
-    "-----------\n",
     "\n",
     "This notebook shows how to use `dysh` to smooth a spectrum.   For the example below we will use data from the Position-Switch example. The following dysh commands are the simplest to get and smooth a spectrum (leaving out all the function arguments):\n",
     "\n",
@@ -793,7 +792,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.0"
+   "version": "3.10.0"
   },
   "toc": {
    "base_numbering": 0

notebooks/examples/subbeamnod.ipynb

@@ -6,7 +6,7 @@
    "metadata": {},
    "source": [
     "# SubBeamNod Data Reduction\n",
-    "---------------------------\n",
+    "\n",
     "This notebook shows how to use `dysh` to calibrate an SubBeamNod observation via two different methods. It retrieves and calibrates SubBeamNod scans using `GBTFITSLoad.subbeamnod()` which returns a `ScanBlock` object. "
    ]
   },
@@ -493,7 +493,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.0"
+   "version": "3.10.0"
   }
  },
  "nbformat": 4,

notebooks/examples/velocity_frames.ipynb

@@ -6,7 +6,6 @@
    "metadata": {},
    "source": [
     "# Spectral Axes, Velocity Frames and Conventions in `dysh`\n",
-    "----------------------------------\n",
     "\n",
     "This notebook shows how to change spectral axes to represent different rest frames and Doppler conventions."
    ]
@@ -877,7 +876,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.0"
+   "version": "3.10.0"
   },
   "toc": {
    "base_numbering": 0

pyproject.toml

@@ -51,6 +51,7 @@ dev = [
   "sphinx-inline-tabs",
   "sphinx-book-theme",
   "sphinx-design",
+  "sphinx-copybutton",
   "sphinxcontrib-mermaid",
   "nbformat",
   "nbclient",

src/dysh/fits/gbtfitsload.py

@@ -1098,7 +1098,7 @@ def getps(
         Returns
         -------
         scanblock : `~spectra.scan.ScanBlock`
-            ScanBlock containing the individual `~spectra.scan.PSScan`s
+            ScanBlock containing one or more `~spectra.scan.PSScan`.
 
         """
 
@@ -1260,7 +1260,7 @@ def getnod(
         Returns
         -------
         scanblock : `~spectra.scan.ScanBlock`
-            ScanBlock containing the individual `~spectra.scan.NodScan`s
+            ScanBlock containing one or more `~spectra.scan.NodScan`.
 
         """
 
@@ -1493,7 +1493,7 @@ def getfs(
         Returns
         -------
         scanblock : `~spectra.scan.ScanBlock`
-            ScanBlock containing the individual `~spectra.scan.FSScan`s
+            ScanBlock containing one or more`~spectra.scan.FSScan`.
 
         """
         debug = kwargs.pop("debug", False)

src/dysh/fits/sdfitsload.py

@@ -407,16 +407,17 @@ def rawspectrum(self, i, bintable=0, setmask=False):
 
         Parameters
         ----------
-            i :  int
-                The row index to retrieve.
-            bintable :  int or None
-                The index of the `bintable` attribute. If None, the underlying bintable is computed from i
-            setmask : bool
-                If True, set the data mask according to the current flags in the `_flagmask` attribute.
+        i :  int
+            The row index to retrieve.
+        bintable :  int or None
+            The index of the `bintable` attribute. If None, the underlying bintable is computed from i
+        setmask : bool
+            If True, set the data mask according to the current flags in the `_flagmask` attribute.
+
         Returns
         -------
-            rawspectrum : ~numpy.ma.MaskedArray
-                The i-th row of DATA column of the input bintable, masked according to `setmask`
+        rawspectrum : ~numpy.ma.MaskedArray
+            The i-th row of DATA column of the input bintable, masked according to `setmask`
 
         """
         if bintable is None:

src/dysh/spectra/core.py

@@ -775,7 +775,7 @@ def data_ishift(y, ishift, axis=-1, remove_wrap=True, fill_value=np.nan):
 
 def data_fshift(y, fshift, method="fft", pad=False, window=True):
     """
-    Shift `y` by `fshift` channels, where |`fshift`|<1.
+    Shift `y` by `fshift` channels, where `abs(fshift)<1`.
 
     Parameters
     ----------

src/dysh/spectra/spectrum.py

@@ -341,22 +341,24 @@ def stats(self, roll=0, qac=False):
 
         Parameters
         ----------
-            roll : int
-                Return statistics on a 'rolled' array differenced with the
-                original array. If there is no correllaton between channels,
-                a roll=1 would return an RMS sqrt(2) larger than that of the
-                input array. Another advantage of rolled statistics it will
-                remove most slow variations, thus RMS/sqrt(2) might be a better
-                indication of the underlying RMS.
-                Default: 0
-            qac : bool
-                If set, the returned simple string contains mean,rms,datamin,datamax
-                for easier visual regression. Based on some legacy code.
-                Default: False
+        roll : int
+            Return statistics on a 'rolled' array differenced with the
+            original array. If there is no correllaton between channels,
+            a roll=1 would return an RMS sqrt(2) larger than that of the
+            input array. Another advantage of rolled statistics it will
+            remove most slow variations, thus RMS/sqrt(2) might be a better
+            indication of the underlying RMS.
+            Default: 0
+        qac : bool
+            If set, the returned simple string contains mean,rms,datamin,datamax
+            for easier visual regression. Based on some legacy code.
+            Default: False
+
         Returns
         -------
         stats : dict
             Dictionary consisting of (mean,median,rms,datamin,datamax)
+
         """
 
         if roll == 0:

src/dysh/util/download.py

@@ -7,6 +7,8 @@
 from rich.progress import Progress
 from tenacity import retry, stop_after_attempt
 
+from dysh.log import init_logging, logger
+
 
 @retry(stop=stop_after_attempt(3))
 def from_url(url, path=Path(".")):
@@ -30,7 +32,6 @@ def from_url(url, path=Path(".")):
     if type(path) is str:
         path = Path(path)
 
-    print(f"Starting download...")
     try:
         # Make the HTTPX client
         client = httpx.Client(follow_redirects=True)
@@ -49,11 +50,12 @@ def from_url(url, path=Path(".")):
 
             # Skip downloading if file already exists
             if savepath.exists():
-                print(f"{filename} already downloaded at {path}")
+                logger.info(f"{filename} already downloaded at {path}")
                 return savepath
 
             else:
                 # Download the file
+                logger.info("Starting download...")
                 resp.raise_for_status()
 
                 # Download to a temporary path first
@@ -62,7 +64,7 @@ def from_url(url, path=Path(".")):
 
                 # Write chunks to file with progress bar
                 with open(tmp_path, "wb") as out_file:
-                    with Progress() as progress:
+                    with Progress(refresh_per_second=5) as progress:
                         task_length = int(resp.headers.get("content-length", 0))
                         task = progress.add_task("[red]Downloading...", total=task_length)
                         for chunk in resp.iter_raw():
@@ -77,7 +79,7 @@ def from_url(url, path=Path(".")):
 
     # Rename the temp file to the desired name
     tmp_path.rename(savepath)
-    print(f"Saved {filename} to {savepath}")
+    logger.info(f"Saved {filename} to {savepath}")
 
     return Path(savepath)
 
@@ -104,4 +106,5 @@ def main():
 
 
 if __name__ == "__main__":
+    init_logging(2)
     main()