Merge 4742062 into f063bb1

.coveragerc

@@ -3,7 +3,8 @@ source=pystart
 branch=True
 omit =
      # Omit large plotting function.
-     eniric/plotting_functions.py
+     eniric/obsolete/plotting_functions.py
+     eniric/obsolete/*
      data/*
      plots/*
      precision/*

.gitignore

@@ -17,6 +17,9 @@ data/atmmodel/Average_TAPAS_2014_visible.txt
 data/atmmodel/Average_TAPAS_2014*.txt
 data/test_data/*
 
+.joblib
+docs/Notebooks/.joblib
+
 # updated_files data
 eniric/updated_code/resampled_cont/*
 # White list one file

appveyor.yml

@@ -30,7 +30,7 @@ install:
   - cmd: "move tests\\config.yaml config.yaml"
 
   # Generate data
-  - cmd: "%PYTHON%\\python.exe eniric_scripts\\make_test_data.py"
+  - cmd: "%PYTHON%\\python.exe eniric\\obsolete\\make_test_data.py"
 
   # Prepare atmosphere models
   - cmd: "%PYTHON%\\python.exe eniric_scripts\\split_atmmodel.py -b ALL"

conftest.py

@@ -6,7 +6,9 @@
 import pytest
 
 import eniric
-from eniric.IOmodule import pdread_2col
+import eniric.io_module as io
+from eniric import utilities as utils
+from eniric.atmosphere import Atmosphere
 
 resampled_template = "Spectrum_{0}-PHOENIX-ACES_{1}band_vsini{2}_R{3}_res3.0.txt"
 
@@ -67,7 +69,7 @@ def resampled_data(request):
     test_data = os.path.join(
         eniric.paths["resampled"], resampled_template.format(star, band, vel, res)
     )
-    wav, flux = pdread_2col(test_data)
+    wav, flux = io.pdread_2col(test_data)
     return id_string, wav, flux
 
 
@@ -124,3 +126,43 @@ def trans_unit(request):
 def grad_flag(request):
     """Gradient flag parameter."""
     return request.param
+
+
+@pytest.fixture(
+    params=[
+        # "Average_TAPAS_2014_H.txt",
+        "Average_TAPAS_2014_K.txt",
+        "Average_TAPAS_2014_J.txt",
+    ]
+)
+def atm_model(request):
+    """Get atmospheric model name to load."""
+    return os.path.join(eniric.paths["atmmodel"], request.param)
+
+
+@pytest.fixture(params=[2.5, 4])
+def atmosphere_fixture(request, atm_model):
+    percent_cutoff = request.param
+    atm = Atmosphere.from_file(atm_model)
+    atm.mask_transmission(percent_cutoff)
+    return atm
+
+
+@pytest.fixture()
+def short_atmosphere(atmosphere_fixture):
+    # First 2000 data points only to speed up tests
+    return atmosphere_fixture[:2000]
+
+
+@pytest.fixture(params=[(0, 1500), (8000, 9000)])
+def sliced_atmmodel_default_mask(request, atm_model):
+    """To do own masking. Sliced in different places."""
+    lower, upper = request.param  # slice limits
+    atm = Atmosphere.from_file(atm_model)
+    return atm[int(lower) : int(upper)]
+
+
+@pytest.fixture(params=[[3900, 4.5, 0, 0], [2600, 4.5, 0, 0]])
+def testing_spectrum(request):
+    wav, flux = utils.load_aces_spectrum(request.param)
+    return wav, flux

docs/Notebooks/barycentric_shift.py

@@ -2,28 +2,31 @@
 # coding: utf-8
 
 # ## Testing barycentric shift in eniric
-# 
+#
 
 # In[ ]:
 
 
 import matplotlib.pyplot as plt
 import numpy as np
+
 # to remove labels in one tick
 from matplotlib.ticker import MaxNLocator
 
-import eniric.IOmodule as IOmodule
+import eniric.io_module as io
 import eniric.Qcalculator as Qcalculator
-from eniric.plotting_functions import (plot_atmosphere_model,
-                                       plot_stellar_spectum)
+from eniric.obsolete.plotting_functions import (
+    plot_atmosphere_model,
+    plot_stellar_spectum,
+)
 from eniric.utilities import band_selector, wav_selector
 
 # In[ ]:
 
 
 def prepare_atmosphere():
     """ Read in atmopheric model and prepare. """
-    wav_atm, flux_atm, std_flux_atm, mask_atm = IOmodule.pdread_4col(atmmodel)
+    wav_atm, flux_atm, std_flux_atm, mask_atm = io.pdread_4col(atmmodel)
     # pandas lready returns numpy arrays
     wav_atm = wav_atm / 1000.0  # conversion from nanometers to micrometers
     mask_atm = np.array(mask_atm, dtype=bool)
@@ -34,40 +37,60 @@ def barycenter_shift(wav_atm, mask_atm, offset_RV=0.0):
     """ Calculating impact of Barycentric movement on mask...
 
     Extends the masked region to +-30 km/s due to the barycentic motion of the earth.
-    
+
     offset_RV: float
         Radial veloctiy offset in km/s.
     """
-    RV_bary = 3.0e4   # 30 km/s barycentric velocity
-    offset_RV = offset_RV * 1.0e3     # Trun offset into m/s
+    RV_bary = 3.0e4  # 30 km/s barycentric velocity
+    offset_RV = offset_RV * 1.0e3  # Trun offset into m/s
     pixels_start = np.sum(mask_atm)
     pixels_total = len(mask_atm)
 
     mask_atm_30kms = []
     for wav_val, mask_val in zip(wav_atm, mask_atm):
-        if (mask_val is False and offset_RV == 666.0):    # if the mask is false and the offset is equal to zero
+        if (
+            mask_val is False and offset_RV == 666.0
+        ):  # if the mask is false and the offset is equal to zero
             mask_atm_30kms.append(mask_val)
 
         else:
-            delta_lambda = wav_val * RV_bary / Qcalculator.c.value    # doppler shift amount   delta_lambda = lambda*v/c
-
-            starting_lambda = wav_val * offset_RV / Qcalculator.c.value   # offset value
-
-            indexes_30kmslice = np.searchsorted(wav_atm, [starting_lambda+wav_val-delta_lambda, starting_lambda+wav_val+delta_lambda])
-
+            delta_lambda = (
+                wav_val * RV_bary / Qcalculator.c.value
+            )  # doppler shift amount   delta_lambda = lambda*v/c
+
+            starting_lambda = wav_val * offset_RV / Qcalculator.c.value  # offset value
+
+            indexes_30kmslice = np.searchsorted(
+                wav_atm,
+                [
+                    starting_lambda + wav_val - delta_lambda,
+                    starting_lambda + wav_val + delta_lambda,
+                ],
+            )
+
             # Replaces any values outside len(wav_atm) with end index value
-            indexes_30kmslice = [index if(index < len(wav_atm)) else len(wav_atm)-1 for index in indexes_30kmslice]
-            mask_atm_30kmslice = np.array(mask_atm[indexes_30kmslice[0]:indexes_30kmslice[1]], dtype=bool)    # selecting only the slice in question
+            indexes_30kmslice = [
+                index if (index < len(wav_atm)) else len(wav_atm) - 1
+                for index in indexes_30kmslice
+            ]
+            mask_atm_30kmslice = np.array(
+                mask_atm[indexes_30kmslice[0] : indexes_30kmslice[1]], dtype=bool
+            )  # selecting only the slice in question
 
             # if(False in mask_atm_30kmslice):
             #    mask_atm_30kms.append(False)
             # else:
             #    mask_atm_30kms.append(True)
 
-            mask_atm_30kmslice_reversed = [not i for i in mask_atm_30kmslice]    # comp list of array is bad
+            mask_atm_30kmslice_reversed = [
+                not i for i in mask_atm_30kmslice
+            ]  # comp list of array is bad
             print("mask_atm_30kmslice_reversed", mask_atm_30kmslice_reversed)
-
-            clump = np.array_split(mask_atm_30kmslice, np.where(np.diff(mask_atm_30kmslice_reversed))[0]+1)[::2]
+
+            clump = np.array_split(
+                mask_atm_30kmslice,
+                np.where(np.diff(mask_atm_30kmslice_reversed))[0] + 1,
+            )[::2]
             print("clump", clump)
             tester = True
             for block in clump:
@@ -79,8 +102,11 @@ def barycenter_shift(wav_atm, mask_atm, offset_RV=0.0):
 
     mask_atm = np.array(mask_atm_30kms, dtype=bool)
     pixels_end = np.sum(mask_atm)
-    print(("Barycentric impact masks out {:04.1}\% more of the atmospheric"
-          " spectrum").format((pixels_end-pixels_start)/pixels_total))
+    print(
+        (
+            "Barycentric impact masks out {:04.1}\% more of the atmospheric" " spectrum"
+        ).format((pixels_end - pixels_start) / pixels_total)
+    )
     return mask_atm
 
 
@@ -90,6 +116,7 @@ def barycenter_shift(wav_atm, mask_atm, offset_RV=0.0):
 def inner_function():
     pass
 
+
 def new_inner_function():
     pass
 
@@ -129,44 +156,62 @@ def new_inner_function():
 pixels_total = len(mask_atm)
 print(pixels_start, pixels_total)
 
-offset_RV=0
+offset_RV = 0
 
 mask_atm_30kms = []
 for wav_val, mask_val in zip(wav_atm, mask_atm):
-        if (mask_val is False and offset_RV == 666.0):    # if the mask is false and the offset is equal to zero
-            mask_atm_30kms.append(mask_val)
-
-        else:
-            delta_lambda = wav_val * 3.0e4 / Qcalculator.c.value
-            print("delta_lambda", delta_lambda)
-
-            starting_lambda = wav_val * offset_RV * 1.0e3 / Qcalculator.c.value
-            print("starting_lambda", starting_lambda)
-
-            indexes_30kmslice = np.searchsorted(wav_atm, [starting_lambda+wav_val-delta_lambda, starting_lambda+wav_val+delta_lambda])
-
-            indexes_30kmslice = [index if(index < len(wav_atm)) else len(wav_atm)-1 for index in indexes_30kmslice]
-
-            mask_atm_30kmslice = np.array(mask_atm[indexes_30kmslice[0]:indexes_30kmslice[1]], dtype=bool)    # selecting only the slice in question
-
-            # if(False in mask_atm_30kmslice):
-            #    mask_atm_30kms.append(False)
-            # else:
-            #    mask_atm_30kms.append(True)
-
-            mask_atm_30kmslice_reversed = [not i for i in mask_atm_30kmslice]
-
-            clump = np.array_split(mask_atm_30kmslice, np.where(np.diff(mask_atm_30kmslice_reversed))[0]+1)[::2]
-
-            tester = True
-            for block in clump:
-                if len(clump) >= 3:
-                    tester = False
-                    break
-
-            mask_atm_30kms.append(tester)
+    if (
+        mask_val is False and offset_RV == 666.0
+    ):  # if the mask is false and the offset is equal to zero
+        mask_atm_30kms.append(mask_val)
+
+    else:
+        delta_lambda = wav_val * 3.0e4 / Qcalculator.c.value
+        print("delta_lambda", delta_lambda)
+
+        starting_lambda = wav_val * offset_RV * 1.0e3 / Qcalculator.c.value
+        print("starting_lambda", starting_lambda)
+
+        indexes_30kmslice = np.searchsorted(
+            wav_atm,
+            [
+                starting_lambda + wav_val - delta_lambda,
+                starting_lambda + wav_val + delta_lambda,
+            ],
+        )
+
+        indexes_30kmslice = [
+            index if (index < len(wav_atm)) else len(wav_atm) - 1
+            for index in indexes_30kmslice
+        ]
+
+        mask_atm_30kmslice = np.array(
+            mask_atm[indexes_30kmslice[0] : indexes_30kmslice[1]], dtype=bool
+        )  # selecting only the slice in question
+
+        # if(False in mask_atm_30kmslice):
+        #    mask_atm_30kms.append(False)
+        # else:
+        #    mask_atm_30kms.append(True)
+
+        mask_atm_30kmslice_reversed = [not i for i in mask_atm_30kmslice]
+
+        clump = np.array_split(
+            mask_atm_30kmslice, np.where(np.diff(mask_atm_30kmslice_reversed))[0] + 1
+        )[::2]
+
+        tester = True
+        for block in clump:
+            if len(clump) >= 3:
+                tester = False
+                break
+
+        mask_atm_30kms.append(tester)
 
 mask_atm = np.array(mask_atm_30kms, dtype=bool)
 pixels_end = np.sum(mask_atm)
-print(("Barycentric impact masks out {:04.1}\% more of the atmospheric"
-          " spectrum").format((pixels_end-pixels_start)/pixels_total))
+print(
+    (
+        "Barycentric impact masks out {:04.1}\% more of the atmospheric" " spectrum"
+    ).format((pixels_end - pixels_start) / pixels_total)
+)

eniric/__init__.py

@@ -1,9 +1,7 @@
 __version__ = "0.6-beta"
 __all__ = [
     "atmosphere",
-    "IOmodule",
-    "nIRanalysis",
-    "plotting_functions",
+    "io_module",
     "Qcalculator",
     "resample",
     "snr_normalization",