Merge pull request #293 from mfixstsci/numpy-update-fixes

Numpy Update (Master)

CHANGES.rst

@@ -1,4 +1,3 @@
-Changes included in this version
---------------------------------
-
-Edit this template to detail updates to the codebase
+v0.19.1
+-------
+- Patch for new numpy version release (1.25.0). This version deprecated np.int and np.float. This release removes mention of these old methods.

README.md

@@ -133,7 +133,7 @@ The following describes the typical work flow for contributing to the pysiaf pro
 11. Delete your local copy of your branch.
 
 ### Installation  
-This package is supported in python 3.7, 3.8 and 3.9
+This package is supported in python 3.8 and 3.9
 
 `pip install pysiaf`
 

generate/generate_fgs.py

@@ -129,7 +129,7 @@
         polynomial_coefficients = iando.read.read_siaf_distortion_coefficients(instrument, AperName)
 
         number_of_coefficients = len(polynomial_coefficients)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
 
         # set polynomial coefficients
         siaf_indices = ['{:02d}'.format(d) for d in polynomial_coefficients['siaf_index'].tolist()]

generate/generate_nircam.py

@@ -108,7 +108,7 @@
         polynomial_coefficients = iando.read.read_siaf_distortion_coefficients(instrument, AperName)
 
         number_of_coefficients = len(polynomial_coefficients)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
         aperture.Sci2IdlDeg = polynomial_degree
 
         # set polynomial coefficients
@@ -163,8 +163,8 @@
                 if (sca_name == 'NRCA5') and (('MASK335R' in aperture.AperName) or ('MASK430R' in aperture.AperName)):
                     # see https://jira.stsci.edu/browse/JWSTSIAF-77
                     sca_name += '335R430R'
-                v2_offset = np.float(wedge_offsets['v2_offset'][wedge_offsets['name'] == sca_name])
-                v3_offset = np.float(wedge_offsets['v3_offset'][wedge_offsets['name'] == sca_name])
+                v2_offset = float(wedge_offsets['v2_offset'][wedge_offsets['name'] == sca_name])
+                v3_offset = float(wedge_offsets['v3_offset'][wedge_offsets['name'] == sca_name])
                 aperture.V2Ref += v2_offset
                 aperture.V3Ref += v3_offset
             elif dependency_type == 'dhspil_wedge':

generate/generate_niriss.py

@@ -101,7 +101,7 @@
         polynomial_coefficients = iando.read.read_siaf_distortion_coefficients(instrument, AperName)
 
         number_of_coefficients = len(polynomial_coefficients)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
 
         # set polynomial coefficients
         siaf_indices = ['{:02d}'.format(d) for d in polynomial_coefficients['siaf_index'].tolist()]

generate/generate_nirspec.py

@@ -297,7 +297,7 @@ def read_pcf_gtp(file_name):
     # transform to numpy array when possible
     for key in data.keys():
         try:
-            data[key] = np.array(data[key][0].split()).astype(np.float)
+            data[key] = np.array(data[key][0].split()).astype(float)
         except:
             pass
 
@@ -802,7 +802,7 @@ def rows(pcfName, new_pcf_format=False):
     # 'F140X_GWA_OTE', 'F110W_GWA_OTE', 'CLEAR_GWA_OTE']
     elif AperName in pcf_file_mapping.keys():
         number_of_coefficients = len(pcf_data[AperName]['A'])
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
         aperture.Sci2IdlDeg = polynomial_degree
         k = 0
         # polynomial coefficients for transformation that goes directly from the GWA pupil plane to the sky
@@ -816,10 +816,10 @@ def rows(pcfName, new_pcf_format=False):
 
         # coefficients to apply the reflection in the MIRROR taking into account the correction
         # to the GWA position as derived from the sensor readings and their calibration relation
-        aperture.XSciScale = np.float(disperser_mirror_tiltx['CoeffsTemperature00'][0])
-        aperture.YSciScale = np.float(disperser_mirror_tilty['CoeffsTemperature00'][0])
-        aperture.XSciRef = np.float(disperser_mirror_tiltx['Zeroreadings'][0])
-        aperture.YSciRef = np.float(disperser_mirror_tilty['Zeroreadings'][0])
+        aperture.XSciScale = float(disperser_mirror_tiltx['CoeffsTemperature00'][0])
+        aperture.YSciScale = float(disperser_mirror_tilty['CoeffsTemperature00'][0])
+        aperture.XSciRef = float(disperser_mirror_tiltx['Zeroreadings'][0])
+        aperture.YSciRef = float(disperser_mirror_tilty['Zeroreadings'][0])
         aperture.DDCName = 'None'
 
     # TRANSFORM apertures for the conversion between the OTE image plane and the MSA plane
@@ -838,7 +838,7 @@ def rows(pcfName, new_pcf_format=False):
         fore_pcf_data = read_pcf_gtp(fore_pcf)
 
         # deal with different formats of the .pcf files
-        fore_year = np.int(fore_pcf_data['DATE'][0][0:4])
+        fore_year = int(fore_pcf_data['DATE'][0][0:4])
         if fore_year > 2016:
             new_pcf_format = True
         else:

generate/generate_reference_files.py

@@ -669,7 +669,7 @@ def generate_siaf_pre_flight_reference_files_nircam():
 
             #generate distortion reference file
             number_of_coefficients = len(A)
-            polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+            polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
             siaf_index = []
             exponent_x = []
             exponent_y = []
@@ -1143,7 +1143,7 @@ def generate_siaf_pre_flight_reference_files_niriss(distortion_file_name, verbos
 
 
         number_of_coefficients = len(AR)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
 
         # if oss is False:
         if 1:
@@ -1294,7 +1294,7 @@ def generate_siaf_pre_flight_reference_files_fgs(verbose=False, mode='siaf'):
                  -2.81501600E-15, -1.73025000E-15, 2.57732600E-15, 1.75268080E-15, 2.95238320E-15])
 
         number_of_coefficients = len(A)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
 
         # generate distortion coefficient files
         siaf_index = []

pysiaf/aperture.py

@@ -288,7 +288,7 @@ def set_distortion_coefficients_from_file(self, file_name):
         polynomial_coefficients = read.read_siaf_distortion_coefficients(file_name=file_name)
 
         number_of_coefficients = len(polynomial_coefficients)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
         self.Sci2IdlDeg = polynomial_degree
 
         # set polynomial coefficients
@@ -910,7 +910,7 @@ def distortion_transform(self, from_system, to_system, include_offset=True):
         # Get the coefficients for "science" to "ideal" transformation (and back)
 
         # degree of distortion polynomial
-        degree = np.int(getattr(self, 'Sci2IdlDeg'))
+        degree = int(getattr(self, 'Sci2IdlDeg'))
 
         number_of_coefficients = polynomial.number_of_coefficients(degree)
         all_keys = self.__dict__.keys()
@@ -1513,8 +1513,8 @@ def dms_corner(self):
         This corresponds to the OSS corner position (x: ColCorner, y: RowCorner).
         The notation for OSS is 1-based, i.e. the lower left corner of a FULL subarray is (1,1)
         """
-        col_corner = np.ceil(np.min(self.corners('det')[0])).astype(np.int_)
-        row_corner = np.ceil(np.min(self.corners('det')[1])).astype(np.int_)
+        col_corner = np.ceil(np.min(self.corners('det')[0])).astype(int)
+        row_corner = np.ceil(np.min(self.corners('det')[1])).astype(int)
 
         return col_corner, row_corner
 

pysiaf/iando/read.py

@@ -126,11 +126,11 @@ def read_hst_siaf(file=None, version=None):
             a = aperture.HstAperture()
             # Process the first 'CAJ' record.
             a.ap_name = text[0:10].strip()  # Aperture Identifier.
-            a.v2_cent = np.float(text[10:25])  # SICS V2 Center. (same as a_v2_ref)
-            a.v3_cent = np.float(text[25:40])  # SICS V3 Center. (same as a_v3_ref)
+            a.v2_cent = float(text[10:25])  # SICS V2 Center. (same as a_v2_ref)
+            a.v3_cent = float(text[25:40])  # SICS V3 Center. (same as a_v3_ref)
             a.a_shape = text[40:44]  # Aperture Shape.
             try:
-                a.maj = np.float(text[44:59])  # Major Axis Dimension.
+                a.maj = float(text[44:59])  # Major Axis Dimension.
             except ValueError:  # when field is empty
                 a.maj = None
             a.Mac_Flag = text[59]  # !SI Macro Aperture Flag.
@@ -144,24 +144,24 @@ def read_hst_siaf(file=None, version=None):
         elif (text.rstrip()[-3::] == 'CAJ') & (CAJ_index == 1):
             # Process the second 'CAJ' record.
             try:
-                a.min = np.float(text[0:15])  # !Minor Axis Dimension.
+                a.min = float(text[0:15])  # !Minor Axis Dimension.
             except ValueError:  # when field is empty
                 a.min = None
-            a.plate_scale = np.float(text[15:30])  # !Arcsecond per Pixel plate scale.
-            a.a_area = np.float(text[30:45])  # !Area of SI Aperture.
-            a.theta = np.float(text[45:60])  # !Aperture Rotation Angle.
+            a.plate_scale = float(text[15:30])  # !Arcsecond per Pixel plate scale.
+            a.a_area = float(text[30:45])  # !Area of SI Aperture.
+            a.theta = float(text[45:60])  # !Aperture Rotation Angle.
             a.SIAS_Flag = text[60]  # !SIAS coordinate system flag. (If set then AK rec.)
             rec_type = text[70:73]  # !Record type.
             CAJ_index = 2
 
         elif (text.rstrip()[-3::] == 'CAJ') & (CAJ_index == 2):
             # Process the third 'CAJ' record.
-            a.im_par = np.int(text[0:2])  # Image Parity.
-            a.ideg = np.int(text[2])  # !Polynomial Degree.
-            a.xa0 = np.float(text[3:18])  # !SIAS X Center. -> like JWST SCIENCE frame
-            a.ya0 = np.float(text[18:33])  # !SIAS Y Center.
-            a.xs0 = np.float(text[33:48])  # !SICS X Center. -> like JWST IDEAL frame
-            a.ys0 = np.float(text[48:63])  # !SICS Y Center.
+            a.im_par = int(text[0:2])  # Image Parity.
+            a.ideg = int(text[2])  # !Polynomial Degree.
+            a.xa0 = float(text[3:18])  # !SIAS X Center. -> like JWST SCIENCE frame
+            a.ya0 = float(text[18:33])  # !SIAS Y Center.
+            a.xs0 = float(text[33:48])  # !SICS X Center. -> like JWST IDEAL frame
+            a.ys0 = float(text[48:63])  # !SICS Y Center.
             rec_type = text[70:73]  # !Record type.
             CAJ_index = 0
 
@@ -174,34 +174,34 @@ def read_hst_siaf(file=None, version=None):
             rec_type = text[70:73]  # !Record type.
 
         elif text.rstrip()[-3::] == 'CAQ':
-            a.v1x = np.float(text[0:15])  # !SICS Vertex 1_X -> like JWST IDEAL frame
-            a.v1y = np.float(text[15:30])  # !SICS Vertex 1_Y
-            a.v2x = np.float(text[30:45])  # !SICS Vertex 2_X
-            a.v2y = np.float(text[45:60])  # !SICS Vertex 2_Y
+            a.v1x = float(text[0:15])  # !SICS Vertex 1_X -> like JWST IDEAL frame
+            a.v1y = float(text[15:30])  # !SICS Vertex 1_Y
+            a.v2x = float(text[30:45])  # !SICS Vertex 2_X
+            a.v2y = float(text[45:60])  # !SICS Vertex 2_Y
             rec_type = text[70:73]  # !Record type.
 
         elif text.rstrip()[-2::] == 'AQ':
-            a.v3x = np.float(text[0:15])  # !SICS Vertex 3_X
-            a.v3y = np.float(text[15:30])  # !SICS Vertex 3_Y
-            a.v4x = np.float(text[30:45])  # !SICS Vertex 4_X
-            a.v4y = np.float(text[45:60])  # !SICS Vertex 4_Y
+            a.v3x = float(text[0:15])  # !SICS Vertex 3_X
+            a.v3y = float(text[15:30])  # !SICS Vertex 3_Y
+            a.v4x = float(text[30:45])  # !SICS Vertex 4_X
+            a.v4y = float(text[45:60])  # !SICS Vertex 4_Y
             rec_type = text[70:73]  # !Record type.
 
         elif text.rstrip()[-2::] == 'AP':
             # FGS pickles
-            a.pi_angle = np.float(text[0:15])  # !Inner Radius Orientation Angle.
-            a.pi_ext = np.float(text[15:30])  # !Angular Extent of the Inner Radius.
-            a.po_angle = np.float(text[30:45])  # !Outer Radius Orientation Angle.
-            a.po_ext = np.float(text[45:60])  # !Angular Extent of the Outer Radius.
+            a.pi_angle = float(text[0:15])  # !Inner Radius Orientation Angle.
+            a.pi_ext = float(text[15:30])  # !Angular Extent of the Inner Radius.
+            a.po_angle = float(text[30:45])  # !Outer Radius Orientation Angle.
+            a.po_ext = float(text[45:60])  # !Angular Extent of the Outer Radius.
             rec_type = text[70:73]  # !Record type.
 
         elif text.rstrip()[-2::] == 'AM':
-            a.a_v2_ref = np.float(text[0:15])  # !V2 Coordinate of Aperture Reference Point.
+            a.a_v2_ref = float(text[0:15])  # !V2 Coordinate of Aperture Reference Point.
             # (same as v2_cent)
-            a.a_v3_ref = np.float(text[15:30])  # !V3 Coordinate of Aperture Reference Point.
+            a.a_v3_ref = float(text[15:30])  # !V3 Coordinate of Aperture Reference Point.
             # (same as v3_cent)
-            a.a_x_incr = np.float(text[30:45])  # !First Coordinate Axis increment.
-            a.a_y_incr = np.float(text[45:60])  # !Second Coordinate Axis increment.
+            a.a_x_incr = float(text[30:45])  # !First Coordinate Axis increment.
+            a.a_y_incr = float(text[45:60])  # !Second Coordinate Axis increment.
 
         elif text.rstrip()[-2::] == 'AN':
             if (a.a_shape == 'PICK') and ('FGS' in a.ap_name):
@@ -229,7 +229,7 @@ def read_hst_siaf(file=None, version=None):
 
         elif (text.rstrip()[-3::] == 'CAK') & (CAK_index == 0):
             # Process the first 'CAK' record.
-            n_polynomial_coefficients = np.int(((a.ideg + 1) * (a.ideg + 2)) / 2)
+            n_polynomial_coefficients = int(((a.ideg + 1) * (a.ideg + 2)) / 2)
             # the order is
             # SIAS to SICS X Transformation.
             # SIAS to SICS Y Transformation.
@@ -238,19 +238,19 @@ def read_hst_siaf(file=None, version=None):
 
             polynomial_coefficients = np.ones((n_polynomial_coefficients, 4)) * -99
             for jj in np.arange(4):
-                polynomial_coefficients[CAK_index, jj] = np.float(text[15 * jj:15 * (jj + 1)])
+                polynomial_coefficients[CAK_index, jj] = float(text[15 * jj:15 * (jj + 1)])
             CAK_index += 1
 
         elif (text.rstrip()[-3::] == 'CAK') & (CAK_index != 0):
             # Process the remaining 'CAK' records
             for jj in np.arange(4):
-                polynomial_coefficients[CAK_index, jj] = np.float(text[15 * jj:15 * (jj + 1)])
+                polynomial_coefficients[CAK_index, jj] = float(text[15 * jj:15 * (jj + 1)])
             CAK_index += 1
 
         elif text.rstrip()[-2::] == 'AK':
             # Process the last polynomial coefficient record.
             for jj in np.arange(4):
-                polynomial_coefficients[CAK_index, jj] = np.float(text[15 * jj:15 * (jj + 1)])
+                polynomial_coefficients[CAK_index, jj] = float(text[15 * jj:15 * (jj + 1)])
             a.polynomial_coefficients = polynomial_coefficients
             CAK_index = 0
 
@@ -415,7 +415,7 @@ def read_jwst_siaf(instrument=None, filename=None, basepath=None):
                     except (TypeError, ValueError) as e:
                         # print('{}: {}: {}'.format(e, node.tag, node.text))
                         if node.tag == 'DetSciYAngle':
-                            value = np.int(float((node.text)))
+                            value = int(float((node.text)))
                         else:
                             raise TypeError
                 elif node.tag in aperture.STRING_ATTRIBUTES:

pysiaf/tests/test_nirspec.py

@@ -72,7 +72,7 @@ def test_against_test_data(siaf=None):
                     tilt = None
                 else:
                     test_header = fits.getheader(test_data_file)
-                    tilt = (np.float(test_header['GWA_XTIL']), np.float(test_header['GWA_YTIL']))
+                    tilt = (float(test_header['GWA_XTIL']), float(test_header['GWA_YTIL']))
 
                 if sca_name == 'SCA491':
                     AperName = 'NRS1_FULL_OSS'

pysiaf/utils/polynomial.py

@@ -375,7 +375,7 @@ def jacob(a, b, x, y):
 def number_of_coefficients(poly_degree):
     """Return number of coefficients corresponding to polynomial degree."""
     if type(poly_degree) == int:
-        n_coefficients = np.int((poly_degree + 1) * (poly_degree + 2) / 2)
+        n_coefficients = int((poly_degree + 1) * (poly_degree + 2) / 2)
         return n_coefficients
     else:
         raise TypeError('Argument has to be of type int')
@@ -486,7 +486,7 @@ def polynomial_degree(number_of_coefficients):
     if not poly_degree.is_integer():
         raise ValueError('Number of coefficients does not match a valid polynomial degree.')
     else:
-        return np.int(poly_degree)
+        return int(poly_degree)
 
 
 def prepend_rotation_to_polynomial(a, theta, verbose=False):

pysiaf/utils/tools.py

@@ -67,7 +67,7 @@ def compute_roundtrip_error(A, B, C, D, offset_x=0., offset_y=0., verbose=False,
 
     """
     number_of_coefficients = len(A)
-    polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+    polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
     order = polynomial_degree
 
     # regular grid of points (in science pixel coordinates) in the full frame science frame
@@ -440,7 +440,7 @@ def set_reference_point_and_distortion(instrument, aperture, parent_aperture):
 
     """
     polynomial_degree = parent_aperture.Sci2IdlDeg
-    number_of_coefficients = np.int((polynomial_degree + 1) * (polynomial_degree + 2) / 2)
+    number_of_coefficients = int((polynomial_degree + 1) * (polynomial_degree + 2) / 2)
 
     k = 0
     sci2idlx_coefficients = np.zeros(number_of_coefficients)