Simplify extract_bs call.

amical/__init__.py

@@ -1,7 +1,7 @@
 from .analysis.easy_candid import fit_binary, getContrastLimit
 from .core import calibrate
 from .mf_pipeline.ami_function import make_mf
-from .mf_pipeline.bispect import extract_bs_mf
+from .mf_pipeline.bispect import extract_bs
 from .oifits import cal2dict, data2obs, load, loadc, save, show
 
 __version__ = "0.3dev"

amical/mf_pipeline/bispect.py

@@ -35,8 +35,8 @@
 warnings.filterwarnings("ignore")
 
 
-def extract_bs_mf(cube, filename, maskname, filtname=None, targetname=None, bs_MultiTri=False, n_blocks=0, peakmethod='gauss',
-                  hole_diam=0.8, cutoff=1e-4, fw_splodge=0.7, naive_err=False, n_wl=3, verbose=False, display=True,):
+def extract_bs(cube, filename, maskname, filtname=None, targetname=None, bs_MultiTri=False, n_blocks=0, peakmethod='gauss',
+               hole_diam=0.8, cutoff=1e-4, fw_splodge=0.7, naive_err=False, n_wl=3, verbose=False, display=True,):
     """Compute bispectrum (bs, v2, cp, etc.) from a data cube.
 
     Parameters:

amical/tools.py

@@ -627,7 +627,7 @@ def sphere_parang(hdr):
 
 def checkSeeingCond(list_nrm):
     """ Extract the seeing conditions, parang, averaged vis2
-    and cp of a list of nrm classes extracted with extract_bs_mf
+    and cp of a list of nrm classes extracted with extract_bs
     function (bispect.py).
 
     Output

example_NIRISS.py

@@ -37,7 +37,7 @@
 # groundbased observations.
 # ----------------------------------
 
-#  AMI parameters (refer to the docstrings of `extract_bs_mf` for details)
+#  AMI parameters (refer to the docstrings of `extract_bs` for details)
 params_ami = {"peakmethod": 'gauss',
               "bs_MultiTri": False,
               "maskname": "g7",
@@ -46,10 +46,10 @@
 
 # Extract raw complex observables for the target and the calibrator:
 # It's the core of the pipeline (amical/mf_pipeline/bispect.py)
-bs_t = amical.extract_bs_mf(cube_t, file_t, targetname='fakebinary',
-                            **params_ami, display=True)
-bs_c = amical.extract_bs_mf(cube_c, file_c, targetname='fakepsf',
-                            **params_ami, display=False)
+bs_t = amical.extract_bs(cube_t, file_t, targetname='fakebinary',
+                         **params_ami, display=True)
+bs_c = amical.extract_bs(cube_c, file_c, targetname='fakepsf',
+                         **params_ami, display=False)
 
 # Calibrate the raw data to get get calibrated V2 and CP
 # bs_c can be a single calibrator result or a list of calibrator.
@@ -68,6 +68,7 @@
 # So we imposed ncore=1 by default (no multiproc), you can
 # try to increase ncore option in fit_binary but it could crash
 # depending on your system (tested on OSX-mojave).
-fit = amical.fit_binary(s[1], step=50, verbose=False, ncore=1)
+if False:
+    fit = amical.fit_binary(s[1], step=50, verbose=False, ncore=1)
 
 plt.show(block=True)

example_SPHERE.py

@@ -23,7 +23,7 @@
                          corr_ghost=False,
                          display=True)[0]
 
-#  AMI parameters (refer to the docstrings of `extract_bs_mf` for details)
+#  AMI parameters (refer to the docstrings of `extract_bs` for details)
 params_ami = {"peakmethod": 'gauss',
               "bs_MultiTri": False,
               "maskname": "g7",
@@ -34,10 +34,10 @@
 
 # # Extract raw complex observables for the target and the calibrator:
 # # It's the core of the pipeline (amical/mf_pipeline/bispect.py)
-bs_t = amical.extract_bs_mf(cube_t, file_t, targetname='HD142527',
-                            **params_ami, display=True)
-bs_c = amical.extract_bs_mf(cube_c, file_c, targetname='HD142695',
-                            **params_ami, display=False)
+bs_t = amical.extract_bs(cube_t, file_t, targetname='HD142527',
+                         **params_ami, display=True)
+bs_c = amical.extract_bs(cube_c, file_c, targetname='HD142695',
+                         **params_ami, display=False)
 
 # In case of multiple files for a same target, you can
 # check the seeing condition and select only the good ones.