wrapping in docstrings

small fix to timebase plotting in binary_system.py

modules/data_manager.py

@@ -23,7 +23,6 @@
 import numpy as np
 
 import modules.constants as cst
-
 import modules.spinOS_io as spl
 import modules.utils as util
 
@@ -46,7 +45,7 @@ def buildSets(self):
         for dataset in self.datasets['AS']:
             dataset.setData()
         self.setDefWeight()
-        self.gui.def_as_weight.set(self.defWeight)
+        self.gui.def_as_weight.set(np.round(self.defWeight, 4))
 
     def getBuiltRV1s(self):
         data = None
@@ -191,19 +190,19 @@ def setDefWeight(self):
             else:
                 numrv1 = sum(
                     (
-                    len(dataset.getData()) if dataset.getData() is not None
-                    else 0
-                    for dataset in
-                    self.datasets['RV1']))
+                        len(dataset.getData()) if dataset.getData() is not None
+                        else 0
+                        for dataset in
+                        self.datasets['RV1']))
             if not self.hasRV2():
                 numrv2 = 0
             else:
                 numrv2 = sum(
                     (
-                    len(dataset.getData()) if dataset.getData() is not None
-                    else 0
-                    for dataset in
-                    self.datasets['RV2']))
+                        len(dataset.getData()) if dataset.getData() is not None
+                        else 0
+                        for dataset in
+                        self.datasets['RV2']))
             self.defWeight = numas / (numrv1 + numrv2 + numas)
 
 
@@ -230,7 +229,7 @@ def __init__(self, dataman, tab, book, filename, name=None, tpe='AS'):
                        command=self.selAll).grid()
         but = ttk.Frame(newset)
         ttk.Button(but, text='+', command=self.addentry).grid()
-        ttk.Button(but, text='Rename', command=self.setName)\
+        ttk.Button(but, text='Rename', command=self.setName) \
             .grid(row=0, column=1)
         but.pack()
         self.data = None
@@ -276,6 +275,7 @@ def getData(self) -> np.ndarray:
     def selAll(self):
         for entry in self.entries:
             entry.include.set(self.selall.get())
+        self.dataman.buildSets()
 
 
 class RVDataSet(DataSet):

modules/minimizer.py

@@ -135,11 +135,17 @@ def LMminimizer(guess_dict: dict, data_dict: dict, method: str = 'leastsq',
         if not AS:
             for key in 'i', 'Omega', 'mt':
                 params[key].set(vary=False)
+        elif AS and ('q' in params.valuesdict().keys()) \
+                and params.valuesdict()['q'] != 0:
+            params['i'] \
+                .set(expr='180-180/pi*asin(sqrt(1-e**2)*k1*(q+1)/q*'
+                          '(p*86400/(2*pi*6.67430e-20*mt*1.9885e30))**(1/3))')
+
     elif AS:
         for key in 'k1', 'gamma1', 'k2', 'gamma2':
             params[key].set(vary=False)
     else:
-        raise ValueError('No data supplied! Cannot minimize.')
+        raise ValueError('No data supplied! Cannot minimize.\n')
 
     # build a minimizer object
     minimizer = lm.Minimizer(fcn2min, params,
@@ -165,9 +171,8 @@ def LMminimizer(guess_dict: dict, data_dict: dict, method: str = 'leastsq',
         print('this minimization method not implemented')
         return
     toc = time.time()
-    print('Minimization Complete in {} s!\n'.format(toc - tic))
+    print('Minimization Complete in {} s!\n'.format(np.round(toc - tic, 3)))
     lm.report_fit(result.params)
-    print('\n')
     rms_rv1, rms_rv2, rms_as = 0, 0, 0
     system = BinarySystem(result.params.valuesdict())
     if RV1:
@@ -178,16 +183,16 @@ def LMminimizer(guess_dict: dict, data_dict: dict, method: str = 'leastsq',
     if RV2:
         # Same for RV2
         rms_rv2 = np.sqrt(np.sum(
-                (system.secondary.radial_velocity_of_hjds(
-                    rv2s[:, 0]) - rv2s[:, 1]) ** 2) / len(rv2s[:, 1]))
+            (system.secondary.radial_velocity_of_hjds(
+                rv2s[:, 0]) - rv2s[:, 1]) ** 2) / len(rv2s[:, 1]))
     if AS:
         # same for AS
         omc2E = np.sum(
             (system.relative.east_of_hjds(aas[:, 0]) - aas[:, 1]) ** 2)
         omc2N = np.sum(
             (system.relative.north_of_hjds(aas[:, 0]) - aas[:, 2]) ** 2)
         rms_as = np.sqrt((omc2E + omc2N) / LAS)
-    print('Minimization complete, check parameters tab for resulting orbit!')
+    print('Minimization complete, check parameters tab for resulting orbit!\n')
     return result, rms_rv1, rms_rv2, rms_as
 
 

modules/plotting.py

@@ -227,15 +227,16 @@ def init_plots(self):
             plt.close(self.rv_fig)
         if self.as_fig is not None:
             plt.close(self.as_fig)
+
         self.rv_fig = plt.figure(num='RV curve')
+        move_figure(self.rv_fig, int(0.37 * self.gui.w) + 10, 0)
+
         self.as_fig = plt.figure(num='Apparent orbit')
+        move_figure(self.as_fig, int(0.37 * self.gui.w) + 10,
+                    int(0.5 * self.gui.h + 10))
+
         self.rv_ax = self.rv_fig.add_subplot(111)
         self.as_ax = self.as_fig.add_subplot(111, aspect=1)
-
-        move_figure(self.rv_fig, int(int(0.37 * self.gui.w) + 10), 0)
-        move_figure(self.as_fig, int(int(0.37 * self.gui.w) + 10),
-                    int(int(0.5 * self.gui.h) + 10))
-
         self.rv_ax.grid(self.do_grids.get())
         self.setup_rv_ax()
         self.as_ax.axhline(linestyle=':', color='black')
@@ -247,8 +248,7 @@ def init_plots(self):
         self.rv_fig.tight_layout()
         self.as_fig.tight_layout()
         plt.ion()  # important: this lets mpl release the event loop to tk,
-        # ie plt.show() doesn't
-        # block
+        # ie plt.show() doesn't block app
         plt.show()
 
     def setup_rv_ax(self):
@@ -436,6 +436,7 @@ def _determine_time_bounds(self):
             data = self.gui.datamanager.getBuiltRV2s()
             m = min(m, min(data[:, 0]))
             mm = max(mm, max(data[:, 0]))
+        print('time bounds', m, mm)
         return m, mm
 
     def plot_gamma1(self):

modules/spinOS_io.py

@@ -25,12 +25,13 @@ def guess_loader(wd: str, guessfile: str) -> dict:
     """
     parses the guess file and determines values and flags for each guess
     :param wd: the working directory
-    :param guessfile: pathname (relative to wd) pointing to the file containing guesses
+    :param guessfile: pathname (relative to wd) pointing to the file
+    containing guesses
     :return: dictionary containing the guesses and flags for each parameter
     """
     wd = check_slash(wd)
-    guesses = np.genfromtxt(wd + guessfile, dtype=None, filling_values=np.nan, usecols=(0, 1, 2),
-                            encoding='utf-8')
+    guesses = np.genfromtxt(wd + guessfile, dtype=None, filling_values=np.nan,
+                            usecols=(0, 1, 2), encoding='utf-8')
     guessdict = dict()
     for i in range(12):
         guessdict[guesses[i][0]] = (guesses[i][1], guesses[i][2])
@@ -54,7 +55,8 @@ def data_loader(wd: str, filetypes: list, filenames: list) -> dict:
     """
     loads data from files into a dictionary
     :param wd: working directory where the files are
-    :param filetypes: data types to load, must be 'RV1file', 'RV2file', or 'ASfile'
+    :param filetypes: data types to load, must be 'RV1file', 'RV2file',
+    or 'ASfile'
     :param filenames: names of the files in question
     :return: data in a dictionary
     """
@@ -95,7 +97,8 @@ def data_loader(wd: str, filetypes: list, filenames: list) -> dict:
 
 def convert_error_ellipse(major, minor, angle):
     """
-    Converts error ellipses to actual east and north errors by a sampling the error ellipse monte-carlo style and
+    Converts error ellipses to actual east and north errors by a sampling
+    the error ellipse monte-carlo style and
     then taking the variance in the east and north directions.
     :param major: length of the major axis of the error ellipse
     :param minor: length of the minor axis of the error ellipse
@@ -107,7 +110,8 @@ def convert_error_ellipse(major, minor, angle):
     sina = np.sin(angle)
     temp_major = np.random.randn(num) * major
     temp_minor = np.random.randn(num) * minor
-    rotated_temp = np.matmul(np.array([[cosa, sina], [-sina, cosa]]), [temp_major, temp_minor])
+    rotated_temp = np.matmul(np.array([[cosa, sina], [-sina, cosa]]),
+                             [temp_major, temp_minor])
     east_error = np.std(rotated_temp[0])
     north_error = np.std(rotated_temp[1])
     return east_error, north_error

modules/utils.py

@@ -32,10 +32,10 @@ class VerticalScrolledFrame:
     ie it needs a master and layout and it can be a master.
     :width:, :height:, :bg: are passed to the underlying Canvas
     :bg: and all other keyword arguments are passed to the inner Frame
-    note that a widget layed out in this frame will have a self.master 3 layers deep,
-    (outer Frame, Canvas, inner Frame) so
-    if you subclass this there is no built in way for the children to access it.
-    You need to provide the controller separately.
+    note that a widget layed out in this frame will have a self.master 3
+    layers deep, (outer Frame, Canvas, inner Frame) so
+    if you subclass this there is no built in way for the children to access
+    it. You need to provide the controller separately.
     """
 
     def __init__(self, master, **kwargs):
@@ -46,7 +46,8 @@ def __init__(self, master, **kwargs):
 
         self.vsb = tk.Scrollbar(self.outer, orient=tk.VERTICAL)
         self.vsb.pack(fill=tk.Y, side=tk.RIGHT)
-        self.canvas = tk.Canvas(self.outer, highlightthickness=0, width=width, height=height, bg=bg)
+        self.canvas = tk.Canvas(self.outer, highlightthickness=0, width=width,
+                                height=height, bg=bg)
         self.canvas.pack(side=tk.LEFT, fill=tk.BOTH, expand=True)
         self.canvas['yscrollcommand'] = self.vsb.set
         # mouse scroll does not seem to work with just "bind"; You have
@@ -59,16 +60,20 @@ def __init__(self, master, **kwargs):
         self.vsb['command'] = self.canvas.yview
 
         self.inner = ttk.Frame(self.canvas, bg=bg)
-        # pack the inner Frame into the Canvas with the topleft corner 4 pixels offset
-        self.canvas_window = self.canvas.create_window((4, 4), window=self.inner, anchor='nw',
+        # pack the inner Frame into the Canvas with the topleft corner 4
+        # pixels offset
+        self.canvas_window = self.canvas.create_window((4, 4),
+                                                       window=self.inner,
+                                                       anchor='nw',
                                                        tags='self.inner')
         self.inner.bind("<Configure>", self._on_frame_configure)
 
         self.outer_attr = set(dir(tk.Widget))
 
     def __getattr__(self, item):
         if item in self.outer_attr:
-            # geometry attributes etc (eg pack, destroy, tkraise) are passed on to self.outer
+            # geometry attributes etc (eg pack, destroy, tkraise) are passed
+            # on to self.outer
             return getattr(self.outer, item)
         else:
             # all other attributes (_w, children, etc) are passed to self.inner
@@ -93,7 +98,7 @@ def _unbind_mouse(self, event=None):
         self.canvas.unbind_all("<MouseWheel>")
 
     def _on_mousewheel(self, event):
-        """Linux uses event.num; Windows / Mac uses event.delta"""
+        # Linux uses event.num; Windows / Mac uses event.delta
         if event.num == 4 or event.delta > 0:
             self.canvas.yview_scroll(-1, "units")
         elif event.num == 5 or event.delta < 0:

rsc/spinOS.mplstyle

@@ -8,12 +8,12 @@ font.serif		: Computer Modern Roman # Times Roman?
 
 # figure options
 axes.labelsize		: medium
-legend.fontsize		: 8
+legend.fontsize		: 5
 legend.frameon		: False
-figure.dpi 		: 200
+figure.dpi 		    : 150
 axes.formatter.use_mathtext : True
 figure.autolayout : True
-figure.figsize		: 7, 2.5
+figure.figsize		: 7, 2.9
 lines.markersize	: 4
 lines.linewidth		: 1.0