stdpipe 0.2.2__tar.gz → 0.2.4__tar.gz

stdpipe-0.2.4/PKG-INFO

@@ -0,0 +1,29 @@
+Metadata-Version: 2.4
+Name: stdpipe
+Version: 0.2.4
+Summary: Simple Transient Detection Pipeline
+Home-page: https://github.com/karpov-sv/stdpipe
+Author: Sergey Karpov
+Author-email: karpov.sv@gmail.com
+License-File: LICENSE.md
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: astropy>=4.1
+Requires-Dist: matplotlib
+Requires-Dist: astroquery>0.4.1
+Requires-Dist: sep
+Requires-Dist: astroscrappy
+Requires-Dist: photutils
+Requires-Dist: statsmodels
+Requires-Dist: tqdm
+Requires-Dist: regions
+Requires-Dist: python-dateutil
+Requires-Dist: requests
+Requires-Dist: sip_tpv
+Requires-Dist: pyfftw
+Dynamic: author
+Dynamic: author-email
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary

{stdpipe-0.2.2 → stdpipe-0.2.4}/setup.py

@@ -3,7 +3,7 @@
 
 from setuptools import setup, find_packages
 
-__version__ = '0.2.2'
+__version__ = '0.2.4'
 
 requirements = [
     'numpy',

{stdpipe-0.2.2 → stdpipe-0.2.4}/stdpipe/catalogs.py

@@ -30,8 +30,8 @@ catalogs = {
     'usnob1': {'vizier': 'I/284/out', 'name': 'USNO-B1'},
     'gsc': {'vizier': 'I/271/out', 'name': 'GSC 2.2'},
     'skymapper': {
-        'vizier': 'II/358/smss',
-        'name': 'SkyMapper DR1.1',
+        'vizier': 'II/379/smssdr4',
+        'name': 'SkyMapper DR4',
         'extra': [
             '_RAJ2000',
             '_DEJ2000',
@@ -46,8 +46,8 @@ catalogs = {
     'vsx': {'vizier': 'B/vsx/vsx', 'name': 'AAVSO VSX'},
     'apass': {'vizier': 'II/336/apass9', 'name': 'APASS DR9'},
     'sdss': {
-        'vizier': 'V/147/sdss12',
-        'name': 'SDSS DR12',
+        'vizier': 'V/154/sdss16',
+        'name': 'SDSS DR16',
         'extra': ['_RAJ2000', '_DEJ2000'],
     },
     'atlas': {
@@ -82,7 +82,7 @@ def get_cat_vizier(
     -  skymapper - SkyMapper DR1.1
     -  vsx - AAVSO Variable Stars Index
     -  apass - AAVSO APASS DR9
-    -  sdss - SDSS DR12
+    -  sdss - SDSS DR16
     -  atlas - ATLAS-RefCat2, compilative all-sky reference catalogue with uniform zero-points in Pan-STARRS-like bands. We augment it with Johnson-Cousins B, V, R and I magnitudes the same way as Pan-STARRS.
     -  usnob1 - USNO-B1
     -  gsc - Guide Star Catalogue 2.2
@@ -218,17 +218,16 @@ def get_cat_vizier(
         )
         pI1, pI2 = (
             [
-                -0.02274814414922734,
-                0.048462952908062046,
-                -0.046965058282604985,
-                -0.19478935830847588,
+                -0.02239162647929074,
+                0.04401240100377888,
+                -0.038500349283596795,
+                -0.19509051168348646
             ],
             [
-                0.025124060889537177,
-                -0.048672562735374666,
-                -1.199591061144479,
-                -0.1947893583084762,
-            ],
+                0.014586929059030904,
+                -0.025228407778416825,
+                -0.21476143248697746,
+                -0.19509051168348637]
         )
 
         cat['Bmag'] = (
@@ -249,7 +248,7 @@ def get_cat_vizier(
         cat['Imag'] = (
             cat['imag']
             + np.polyval(pI1, cat['gmag'] - cat['rmag'])
-            + np.polyval(pI2, cat['imag'] - cat['zmag'])
+            + np.polyval(pI2, cat['rmag'] - cat['imag'])
         )
 
         cat['e_Bmag'] = cat['e_gmag']
@@ -385,90 +384,169 @@ def get_cat_vizier(
         cat['i_SDSS'] = g - (-0.29676 + 0.64728 * bp_rp - 0.10141 * bp_rp ** 2)
 
     elif catalog == 'skymapper':
-        # to PS1
-        for _ in ['u', 'g', 'r', 'i', 'z']:
-            cat[_ + 'mag'] = cat[_ + 'PSF']
+        log("Augmenting the catalogue with Pan-STARRS photometry")
+
+        # SkyMapper DR4 to PS1 griz, my fit based on Pancino et al. (2022)
+        pg1,pg2 = (
+            [
+                -0.07715320986152466,
+                0.2694597282089696,
+                0.04069379065128178,
+                0.01396290714542747
+            ],
+            [
+                0.026097008342026252,
+                -0.14040957287568073,
+                0.133647539780504,
+                0.013962907145427432
+            ]
+        )
+        pr1,pr2 = (
+            [
+                0.08779280979185472,
+                -0.23257704629617004,
+                0.1890698144343673,
+                -0.008125550119663026
+            ],
+            [
+                -0.06273832689338121,
+                0.21909317812693613,
+                -0.23340488268623696,
+                -0.00812555011966309
+            ]
+        )
+        pi1,pi2 = (
+            [
+                0.03553380678975111,
+                -0.021174189684500792,
+                -0.028159666883815007,
+                0.0009748746568893062
+            ],
+            [
+                0.00911922467970264,
+                -0.0362286983251751,
+                0.1403094994141109,
+                0.0009748746568892609
+            ]
+        )
+        pz1,pz2 = (
+            [
+                0.08071260245520126,
+                -0.051693023216670575,
+                -0.0739439627982131,
+                -0.0020460270205769223
+            ],
+            [
+                0.09720715174271254,
+                -0.32063637962189184,
+                0.37918283208242526,
+                -0.0020460270205769305
+            ]
+        )
+
+        cat['gmag'] = (
+            cat['gPSF']
+            + np.polyval(pg1, cat['gPSF'] - cat['rPSF'])
+            + np.polyval(pg2, cat['rPSF'] - cat['iPSF'])
+        )
+        cat['rmag'] = (
+            cat['rPSF']
+            + np.polyval(pr1, cat['gPSF'] - cat['rPSF'])
+            + np.polyval(pr2, cat['rPSF'] - cat['iPSF'])
+        )
+        cat['imag'] = (
+            cat['iPSF']
+            + np.polyval(pi1, cat['gPSF'] - cat['rPSF'])
+            + np.polyval(pi2, cat['rPSF'] - cat['iPSF'])
+        )
+        cat['zmag'] = (
+            cat['zPSF']
+            + np.polyval(pz1, cat['gPSF'] - cat['rPSF'])
+            + np.polyval(pz2, cat['rPSF'] - cat['iPSF'])
+        )
+
+        for _ in ['g', 'r', 'i', 'z']:
             cat['e_' + _ + 'mag'] = cat['e_' + _ + 'PSF']
 
         log("Augmenting the catalogue with Johnson-Cousins photometry")
 
-        # Johnson-Cousins, copy from PS1 above
+        # SkyMapper DR4 to Johnson-Cousins BVRI, my fit based on Pancino et al. (2022)
         pB1, pB2 = (
             [
-                0.10339527794499666,
-                -0.492149523946056,
-                1.2093816061394638,
-                0.061925048331498395,
+                -0.22773918482205113,
+                0.1818124624962873,
+                1.0021365492384895,
+                0.10762635377473588
             ],
             [
-                -0.2571974580267897,
-                0.9211495207523038,
-                -0.8243222108864755,
-                0.0619250483314976,
-            ],
+                -0.004034933919297649,
+                0.08214592357213418,
+                -0.07535454054888649,
+                0.10762635377473558
+            ]
         )
         pV1, pV2 = (
             [
-                -0.011452922062676726,
-                -9.949308251868327e-05,
-                -0.4650511584366353,
-                -0.007076854914511554,
+                -0.02545732895304914,
+                0.03256423830249228,
+                -0.33074199873567045,
+                -0.002938730214382037
             ],
             [
-                0.012749150754020416,
-                0.057554580469724864,
-                -0.09019328095355343,
-                -0.007076854914511329,
-            ],
+                -0.007342074336918033,
+                0.08255055271047995,
+                -0.14349325478829064,
+                -0.0029387302143822
+            ]
         )
         pR1, pR2 = (
             [
-                0.004905242602502597,
-                -0.046545625824660514,
-                0.07830702317352654,
-                -0.08438139204305026,
+                0.07296699439306827,
+                -0.1943702618426095,
+                0.15375263988851387,
+                -0.08547735652048871
             ],
             [
-                -0.07782426914647306,
-                0.14090289318728444,
-                -0.3634922073369279,
-                -0.08438139204305031,
-            ],
+                -0.07378125129406726,
+                0.18462924970775316,
+                -0.40720945890364135,
+                -0.08547735652048903
+            ]
         )
         pI1, pI2 = (
             [
-                -0.02274814414922734,
-                0.048462952908062046,
-                -0.046965058282604985,
-                -0.19478935830847588,
+                -0.00925391710305653,
+                0.046223960182760516,
+                -0.06889215990613289,
+                -0.19321699685334734
             ],
             [
-                0.025124060889537177,
-                -0.048672562735374666,
-                -1.199591061144479,
-                -0.1947893583084762,
-            ],
+                0.01197866152020802,
+                -0.044370062623186206,
+                -0.05231484699406009,
+                -0.19321699685334745
+            ]
         )
 
         cat['Bmag'] = (
-            cat['gmag']
-            + np.polyval(pB1, cat['gmag'] - cat['rmag'])
-            + np.polyval(pB2, cat['rmag'] - cat['imag'])
+            cat['gPSF']
+            + np.polyval(pB1, cat['gPSF'] - cat['rPSF'])
+            + np.polyval(pB2, cat['rPSF'] - cat['iPSF'])
         )
         cat['Vmag'] = (
-            cat['gmag']
-            + np.polyval(pV1, cat['gmag'] - cat['rmag'])
-            + np.polyval(pV2, cat['rmag'] - cat['imag'])
+            cat['gPSF']
+            + np.polyval(pV1, cat['gPSF'] - cat['rPSF'])
+            + np.polyval(pV2, cat['rPSF'] - cat['iPSF'])
         )
         cat['Rmag'] = (
-            cat['rmag']
-            + np.polyval(pR1, cat['gmag'] - cat['rmag'])
-            + np.polyval(pR2, cat['rmag'] - cat['imag'])
+            cat['rPSF']
+            + np.polyval(pR1, cat['gPSF'] - cat['rPSF'])
+            + np.polyval(pR2, cat['rPSF'] - cat['iPSF'])
         )
         cat['Imag'] = (
-            cat['imag']
-            + np.polyval(pI1, cat['gmag'] - cat['rmag'])
-            + np.polyval(pI2, cat['imag'] - cat['zmag'])
+            cat['iPSF']
+            + np.polyval(pI1, cat['gPSF'] - cat['rPSF'])
+            + np.polyval(pI2, cat['rPSF'] - cat['iPSF'])
         )
 
         cat['e_Bmag'] = cat['e_gmag']
@@ -514,7 +592,7 @@ def get_cat_vizier(
         log("Converting the catalogue Sloan magnitudes to Pan-STARRS ones")
 
         # umag, gmag, rmag, imag and zmag are Sloan ugriz magnitudes! Let's get PS1 ones instead
-        # Fits are based on clean Landolt sample from https://arxiv.org/pdf/1203.0297.pdf
+        # Fits are based on clean Landolt sample from https://arxiv.org/pdf/2205.06186
         pg = [-0.030414391501015867, -0.09960002492299584, -0.002910024005294562]
         pr = [-0.009566553708653305, 0.014924591443344211, -0.003928147919030857]
         pi = [-0.010802807724098494, 0.01124900218746879, 0.01274293783734852]
@@ -528,6 +606,16 @@ def get_cat_vizier(
         cat['imag'] = cat['i_SDSS'] + np.polyval(pi, cat['g_SDSS'] - cat['r_SDSS'])
         cat['zmag'] = cat['z_SDSS'] + np.polyval(pz, cat['g_SDSS'] - cat['r_SDSS'])
 
+    elif catalog == 'sdss':
+        log("Converting the catalogue Sloan magnitudes to AB ones")
+
+        # Zero point biases from https://www.sdss4.org/dr16/algorithms/fluxcal/#SDSStoAB
+        cat['umag'] -= 0.04
+        cat['zmag'] += 0.02
+
+        for _ in ['u', 'g', 'r', 'i', 'z']:
+            cat[_ + '_SDSS'] = cat[_ + 'mag']
+
     return cat
 
 

{stdpipe-0.2.2 → stdpipe-0.2.4}/stdpipe/cutouts.py

@@ -91,18 +91,12 @@ def get_cutout(
     image,
     candidate,
     radius,
-    mask=None,
-    background=None,
-    diff=None,
-    template=None,
-    convolved=None,
-    err=None,
-    footprint=None,
     header=None,
     wcs=None,
     time=None,
     filename=None,
     name=None,
+    **kwargs
 ):
     """Create the cutout from one or more image planes based on the candidate object.
 
@@ -114,24 +108,18 @@ def get_cutout(
     :param image: The science image for `image` plane of the cutout
     :param candidate: The candidate object that should at least contain `x` and `y` fields
     :param radius: Cutout radius in pixels. Cutout will have a square shape with :code:`2*ceil(radius) + 1` width
-    :param mask: The mask image for `mask` plane of the cutout, optional
-    :param background: The background for `background` plane of the cutout, optional
-    :param diff: Difference image for `diff` plane of the cutout, optional
-    :param template: Template image for `template` plane of the cutout, optional
-    :param convolved: Convolved template image for `convolved` plane of the cutout, optional
-    :param err: Noise model image for `err` plane of the cutout, optional
-    :param footprint: Candidate footprint (boolean) image for `footprint` plane of the cutout, optional
     :param header: The header for original image. It will be copied to `header` field of the cutout and modified accordingly to properly represent the shape and WCS of the cutout. Optional
     :param wcs: WCS for the original image. Will be copied to `wcs` field of the cutout with appropriate adjustment of the center so that it properly represents the astrometric solution on the cutout. Takes precedence over `header` parameter in defining cutout WCS. Optional
     :param time: Time (:class:`astropy.time.Time` or :class:`datetime.datetime` or a string representation compatible with them) of the original image acquisition, to be copied to `time` field of the cutout. Optional
     :param filename: Filename of the original image, to be stored in `filename` field of the cutout. Optional
     :param name: The object name, to be stored in the `name` field of the cutout. Optional
+    :param \**kwargs: All additional keyword arguments are interpreted as additional image planes (e.g. mask, diff, template etc).
     :returns: Cutout structure as described below.
 
     Cutout is represented by a dictionary with at least the following fields:
 
     - `image` - primary image plane, centered on the candidate position
-    - `mask`, `background`, `diff`, `template`, `convolved`, `err`, `footprint` - corresponding secondary image planes, if provided as parameters to the routine
+    - `mask`, `background`, `diff`, `template`, `convolved`, `err`, `footprint`, etc - corresponding secondary image planes, if provided as parameters to the routine
     - `header` - header of the original image modified to properly represent the cutout WCS, if provided as a parameter to the routine
     - `wcs` - WCS solution for the original image, modified to properly represent the cutout WCS, if provided as a parameter to the routine
     - `meta` - dictionary of additional metadata for the cutout. It will be populated with all fields of the candidate object, plus additionally:
@@ -154,6 +142,10 @@ def get_cutout(
     if wcs is not None:
         cutout['wcs'] = wcs
 
+        # Let's update header info with this WCS
+        astrometry.clear_wcs(crophead, remove_underscored=True, remove_history=True)
+        crophead += wcs.to_header(relax=True)
+
     if crophead is not None:
         cutout['header'] = crophead
 
@@ -162,26 +154,9 @@ def get_cutout(
             cutout['wcs'] = wcs
 
     # Image planes
-    if mask is not None:
-        cutout['mask'] = crop_image_centered(mask, x0, y0, radius)
-
-    if background is not None:
-        cutout['background'] = crop_image_centered(background, x0, y0, radius)
-
-    if diff is not None:
-        cutout['diff'] = crop_image_centered(diff, x0, y0, radius)
-
-    if template is not None:
-        cutout['template'] = crop_image_centered(template, x0, y0, radius)
-
-    if convolved is not None:
-        cutout['convolved'] = crop_image_centered(convolved, x0, y0, radius)
-
-    if err is not None:
-        cutout['err'] = crop_image_centered(err, x0, y0, radius)
-
-    if footprint is not None:
-        cutout['footprint'] = crop_image_centered(footprint, x0, y0, radius)
+    for pname,plane in kwargs.items():
+        if plane is not None and np.ndim(plane) == 2:
+            cutout[pname] = crop_image_centered(plane, x0, y0, radius)
 
     # Metadata
     for _ in candidate.keys():
@@ -229,6 +204,9 @@ def write_cutout(cutout, filename):
             data = None
         elif type(data) == Time or type(data) == datetime.datetime:
             data = Time(data).to_value('fits')
+        elif not np.isscalar(data):
+            # NumPy arrays and like
+            data = repr(np.ma.filled(data))
         elif np.isreal(data) and np.isnan(data):
             data = 'NaN'
         elif np.isreal(data) and not np.isfinite(data):
@@ -260,18 +238,8 @@ def write_cutout(cutout, filename):
     hdus.append(hdu)
 
     # Store imaging data to named extensions
-    for _ in [
-        'image',
-        'template',
-        'convolved',
-        'diff',
-        'adjusted',
-        'mask',
-        'err',
-        'background',
-        'footprint',
-    ]:
-        if _ in cutout:
+    for _ in cutout.keys():
+        if _ not in ['meta', 'header', 'wcs'] and np.ndim(cutout[_]) == 2:
             data = cutout[_]
 
             if data.dtype == bool:
@@ -305,6 +273,10 @@ def load_cutout(filename):
             data = np.nan
         elif data == 'Inf':
             data = np.inf
+        elif isinstance(data, str) and data.startswith('array('):
+            # FIXME: any safer way to convert it back to array?..
+            array = np.array
+            data = eval(data)
 
         cutout['meta'][name] = data
 
@@ -322,6 +294,9 @@ def load_cutout(filename):
 
     hdus.close()
 
+    if cutout['header']:
+        cutout['wcs'] = WCS(cutout['header'])
+
     return cutout
 
 

{stdpipe-0.2.2 → stdpipe-0.2.4}/stdpipe/lcs.py

@@ -158,16 +158,16 @@ class LCs:
                                     self.lcs[_] = []
                                 self.lcs[_].append(__)
 
-            if i % N == 0 and verbose is not None:
+            if i % N == 0 and verbose == True:
                 sys.stdout.write("\r %d points - %d lcs" % (i, len(self.lcs['x'])))
                 sys.stdout.flush()
 
-        if verbose is not None:
+        if verbose == True:
             sys.stdout.write("\n")
             sys.stdout.flush()
 
         for _ in self.lcs.keys():
-            if isinstance(self.lcs[_], list):
+            if isinstance(self.lcs[_], list) and _ not in ['ids']:
                 self.lcs[_] = np.array(self.lcs[_])
 
         self.lcs['ra'], self.lcs['dec'] = astrometry.xyztoradec(