Fix deprecations

* utcnow to now(UTC)
* ndimage.filters is deprecated

src/megaradrp/instrument/components/instrument.py

@@ -12,7 +12,7 @@
 import numpy as np
 from scipy.stats import norm
 import scipy.interpolate as interpol
-from scipy.ndimage.filters import convolve1d
+from scipy.ndimage import convolve1d
 from numina.instrument.hwdevice import HWDevice
 from numina.instrument.simulation.efficiency import Efficiency
 

src/megaradrp/processing/aperture.py

@@ -200,7 +200,8 @@ def run(self, img):
         hdr['history'] = f'Aperture extraction method {method_name}'
         hdr['history'] = f'Aperture extraction with {self.calibid}'
         hdr['history'] = f'Aperture extraction offsets are {self.trace_repr.global_offset.coef.tolist()}'
-        hdr['history'] = f'Aperture extraction time {datetime.datetime.utcnow().isoformat()}'
+        tnow = datetime.datetime.now(datetime.UTC)
+        hdr['history'] = f'Aperture extraction time {tnow.isoformat()}'
 
         # Update Fibers
         fibers_ext = img['FIBERS']

src/megaradrp/processing/diffuselight.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2019-2021 Universidad Complutense de Madrid
+# Copyright 2019-2023 Universidad Complutense de Madrid
 #
 # This file is part of Megara DRP
 #
@@ -39,7 +39,8 @@ def __init__(self, diffuse, datamodel=None, calibid='calibid-unknown',
     def header_update(self, hdr, imgid):
         hdr['NUM-DFL'] = self.calibid
         hdr['history'] = f'Diffuse light correction {imgid}'
-        hdr['history'] = f'Diffuse light correction time {datetime.datetime.utcnow().isoformat()}'
+        tnow = datetime.datetime.now(datetime.UTC)
+        hdr['history'] = f'Diffuse light correction time {tnow.isoformat()}'
 
     def run(self, img):
         imgid = self.get_imgid(img)

src/megaradrp/processing/extractobj.py

@@ -17,7 +17,7 @@
 import astropy.io.fits as fits
 import astropy.units as u
 from scipy.spatial import KDTree
-from scipy.ndimage.filters import gaussian_filter
+from scipy.ndimage import gaussian_filter
 from numina.array.wavecalib.crosscorrelation import periodic_corr1d
 
 # import megaradrp.datamodel as dm

src/megaradrp/processing/fiberflat.py

@@ -55,7 +55,8 @@ def run(self, img):
     def header_update(self, hdr, imgid):
         hdr['NUM-FLT'] = self.calibid
         hdr['history'] = f'Flat correction {imgid}'
-        hdr['history'] = f'Flat correction time {datetime.datetime.utcnow().isoformat()}'
+        tnow = datetime.datetime.now(datetime.UTC)
+        hdr['history'] = f'Flat correction time {tnow.isoformat()}'
 
 
 class FiberFlatCorrector(CommonFlatCorrector):
@@ -74,7 +75,8 @@ def __init__(self, fiberflat, datamodel=None, dtype='float32'):
     def header_update(self, hdr, imgid):
         hdr['NUM-FIBF'] = self.calibid
         hdr['history'] = f'Fiber flat correction {imgid}'
-        hdr['history'] = f'Fiber flat correction time {datetime.datetime.utcnow().isoformat()}'
+        tnow = datetime.datetime.now(datetime.UTC)
+        hdr['history'] = f'Fiber flat correction time {tnow.isoformat()}'
 
 
 class Splitter(Corrector):

src/megaradrp/processing/fluxcalib.py

@@ -68,7 +68,8 @@ def header_update(self, hdr, imgid):
         update_flux_limits(hdr, self.pixlims, ref=0)
 
         hdr['history'] = f'Flux calibration in {imgid}'
-        hdr['history'] = f'Flux calibration time {datetime.datetime.utcnow().isoformat()}'
+        tnow = datetime.datetime.now(datetime.UTC)
+        hdr['history'] = f'Flux calibration time {tnow.isoformat()}'
 
 
 def update_flux_limits(header, pixlims, wcs=None, ref=1):

src/megaradrp/processing/slitflat.py

@@ -28,4 +28,5 @@ def __init__(self, slitflat, datamodel=None, calibid='calibid-unknown',
     def header_update(self, hdr, imgid):
         hdr['NUM-SLTF'] = self.calibid
         hdr['history'] = f'Slit flat correction {imgid}'
-        hdr['history'] = f'Slit flat correction time {datetime.datetime.utcnow().isoformat()}'
+        tnow = datetime.datetime.now(datetime.UTC)
+        hdr['history'] = f'Slit flat correction time {tnow.isoformat()}'

src/megaradrp/processing/tests/test_modelmap.py

@@ -76,7 +76,7 @@ def test_2():
 
 
 def test_calc1():
-    import scipy.sparse.csr
+    import scipy.sparse
     model = GaussBoxModelDescription().model_cls
     g_mean = 100 + 6 * np.arange(623)
     g_std = 1 + np.zeros_like(g_mean)
@@ -86,4 +86,4 @@ def test_calc1():
     params['mean'] = g_mean
     params['stddev'] = g_std
     wm = calc_matrix(wshape, model, params, valid)
-    assert isinstance(wm, scipy.sparse.csr.csr_matrix)
+    assert isinstance(wm, scipy.sparse.csr_matrix)

src/megaradrp/processing/trimover.py

@@ -7,7 +7,7 @@
 # License-Filename: LICENSE.txt
 #
 
-from __future__ import print_function, division
+from __future__ import division
 
 import logging
 import datetime
@@ -29,10 +29,9 @@
 
 def trimOut(img, detconf, direction='normal', out='trimmed.fits'):
     """
-    :param data: original data to be trimmed. Can be either a string <path>, an ImageHDU or a numpy array
+    :param img: original data to be trimmed. Can be either a string <path>, an ImageHDU or a numpy array
     :param direction: Can be either 'normal' or 'mirror'
     :param out: When the original data is a path, the returned value is a file too
-    :param bins: is the index of the _binning dictionary
     :return:
     """
 
@@ -92,8 +91,8 @@ def direcfun(x): return x
     return finaldata
 
 
-def get_conf_value(confFile, key):
-    return confFile[key]
+def get_conf_value(conf_file, key):
+    return conf_file[key]
 
 
 def apextract_weights(data, weights, size=4096):
@@ -103,7 +102,7 @@ def apextract_weights(data, weights, size=4096):
 
     def decompress(tar_file):
         """
-        :param tar_name: <str> name of the tar file
+        :param tar_file: <str> name of the tar file
         :return: None
         """
 
@@ -198,10 +197,10 @@ def __init__(self, detconf, datamodel=None, calibid='calibid-unknown', dtype='fl
                                                 dtype=dtype)
 
     def data_binning(self, data, binning):
-        '''
+        """
          Axis:x --> factorX
          Axis:y --> factorY
-        '''
+        """
         factorX = 1.0 / binning[1]
         factorY = 1.0 / binning[0]
         x = int(factorY * data[0][0])
@@ -212,8 +211,6 @@ def data_binning(self, data, binning):
         return x, y, z, t
 
     def test_image(self):
-        import astropy.io.fits as fits
-
         data = np.empty((4212, 4196), dtype='float32')
         data[self.pcol1] += 1
         data[self.orow1] += 10
@@ -253,7 +250,8 @@ def run(self, img):
         hdr = img['primary'].header
         hdr['NUM-OVPE'] = self.calibid
         hdr['history'] = f'Overscan correction with {self.calibid}'
-        hdr['history'] = f'Overscan correction time {datetime.datetime.utcnow().isoformat()}'
+        tnow = datetime.datetime.now(datetime.UTC)
+        hdr['history'] = f'Overscan correction time {tnow.isoformat()}'
         # hdr['history'] = 'Mean of prescan1 is %f' % p1
         hdr['history'] = f'Median of col overscan1 is {oc1}'
         hdr['history'] = "Overscan1 correction is spline3"
@@ -320,7 +318,8 @@ def run(self, img):
         hdr = img['primary'].header
         hdr['NUM-TRIM'] = self.calibid
         hdr['history'] = f'Trimming correction with {self.calibid}'
-        hdr['history'] = f'Trimming correction time {datetime.datetime.utcnow().isoformat()}'
+        tnow = datetime.datetime.now(datetime.UTC)
+        hdr['history'] = f'Trimming correction time {tnow.isoformat()}'
 
         return img
 
@@ -353,7 +352,8 @@ def run(self, img):
         img[0].data[part:] *= self.gain2
 
         hdr['history'] = f'Gain correction with {self.calibid}'
-        hdr['history'] = f'Gain correction time {datetime.datetime.utcnow().isoformat()}'
+        tnow = datetime.datetime.now(datetime.UTC)
+        hdr['history'] = f'Gain correction time {tnow.isoformat()}'
         hdr['history'] = f'Gain1 correction value {self.gain1}'
         hdr['history'] = f'Gain2 correction value {self.gain2}'
         return img

src/megaradrp/processing/twilight.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2011-2021 Universidad Complutense de Madrid
+# Copyright 2011-2023 Universidad Complutense de Madrid
 #
 # This file is part of Megara DRP
 #
@@ -59,6 +59,6 @@ def run(self, img):
     def header_update(self, hdr, imgid):
         hdr['NUM-TWIF'] = self.calibid
         cap = self.flattag.capitalize()
-        now = datetime.datetime.utcnow().isoformat()
+        now = datetime.datetime.now(datetime.UTC).isoformat()
         hdr['history'] = f'{cap} flat correction {imgid}'
         hdr['history'] = f'{cap} flat correction time {now}'

src/megaradrp/processing/wavecalibration.py

@@ -10,7 +10,7 @@
 """Corrector for wavelength calibration"""
 
 import logging
-import datetime
+from datetime import datetime, UTC
 import warnings
 import uuid
 
@@ -185,7 +185,7 @@ def calibrate_wl_rss(rss, solutionwl, npix, targetwcs, dtype='float32', span=0,
     hdr['history'] = f'Wavelength calibration with {solutionwl.calibid}'
     hdr['history'] = 'Aperture extraction offsets are {}'.format(
         solutionwl.global_offset.coef.tolist())
-    hdr['history'] = f'Wavelength calibration time {datetime.datetime.utcnow().isoformat()}'
+    hdr['history'] = f'Wavelength calibration time {datetime.now(UTC).isoformat()}'
     hdr['history'] = f'Resample span={span}'
     # Update UUID
     hdr['UUID'] = str(uuid.uuid1())

src/megaradrp/recipes/calibration/bpm.py

@@ -56,12 +56,12 @@ class BadPixelsMaskRecipe(MegaraBaseRecipe):
 
     def run(self, rinput):
         self.logger.info('start BPM recipe')
-        N = len(rinput.obresult.frames)
+        nframes = len(rinput.obresult.frames)
 
-        self.logger.debug('we have %d images', N)
-        half = N // 2
+        self.logger.debug('we have %d images', nframes)
+        half = nframes // 2
         flow = self.init_filters(rinput, rinput.obresult.configuration)
-        self.logger.debug('we have %d images', N)
+        self.logger.debug('we have %d images', nframes)
         reduced1 = basic_processing_with_combination_frames(
             rinput.obresult.frames[:half],
             flow,
@@ -86,9 +86,8 @@ def run(self, rinput):
 
         self.set_base_headers(hdu.header)
 
-        hdu.header['history'] = 'BPM creation time {}'.format(
-            datetime.datetime.utcnow().isoformat()
-        )
+        tnow = datetime.datetime.now(datetime.UTC)
+        hdu.header['history'] = 'BPM creation time {}'.format(tnow.isoformat())
 
         for frame in rinput.obresult.frames:
             hdu.header['history'] = "With image {}".format(

src/megaradrp/recipes/calibration/slitflat.py

@@ -7,12 +7,12 @@
 # License-Filename: LICENSE.txt
 #
 
-from __future__ import division, print_function
+from __future__ import division
 
 import uuid
 
 import numpy
-from scipy.ndimage.filters import median_filter
+from scipy.ndimage import median_filter
 from astropy.io import fits
 from numina.array import combine
 from numina.core import Result

src/megaradrp/recipes/calibration/trace.py

@@ -9,7 +9,7 @@
 
 """Fiber tracing Recipe."""
 
-from __future__ import division, print_function
+from __future__ import division
 
 import logging
 import warnings
@@ -27,7 +27,7 @@
 from numina.array.wavecalib.crosscorrelation import convolve_comb_lines
 from skimage.filters import threshold_otsu
 from skimage.feature import peak_local_max
-from scipy.ndimage.filters import minimum_filter
+from scipy.ndimage import minimum_filter
 from numina.frame.utils import copy_img
 
 from megaradrp.processing.aperture import ApertureExtractor

src/megaradrp/simulation/factory.py

@@ -9,9 +9,9 @@
 
 """Simple monocromatic simulation"""
 
-import uuid
+import datetime
 import math
-from datetime import datetime
+import uuid
 
 import astropy.wcs as wcs
 import astropy.io.fits as fits
@@ -153,7 +153,8 @@ def create_from_instrument(self, data, name, instrument, mode=''):
         # pheader['FILENAME'] = name
         # OBS mode
         pheader['OBSMODE'] = mode
-        pheader['DATE-OBS'] = datetime.utcnow().isoformat()
+        tnow = datetime.datetime.now(datetime.UTC)
+        pheader['DATE-OBS'] = tnow.isoformat()
         exptime = meta[instrument.name].get('exposed', 1.0)
         pheader['EXPTIME'] = exptime
         pheader['EXPOSED'] = exptime
@@ -169,9 +170,10 @@ def create(self, data, name, control):
         pheader['OBSMODE'] = control.mode
         pheader['UUID'] = str(uuid.uuid4())
         # Date of simulation
-        pheader['DATE'] = datetime.utcnow().isoformat()
+        tnow = datetime.datetime.now(datetime.UTC)
+        pheader['DATE'] = tnow.isoformat()
         # Date of simulated observation, not set yet
-        pheader['DATE-OBS'] = datetime.utcnow().isoformat()
+        pheader['DATE-OBS'] = tnow.isoformat()
 
         # Seqs
         metacontrol = control.config_info()