New TODOs and small changes to environment.yml.

environment.yml

@@ -44,6 +44,7 @@ dependencies:
   # IPython and notebooks:
   - ipython=5.3
   - jupyter=1.0
+  - nb_conda=2.2
   # TODO: Add back GUI dependencies!
   # TODO: Get Jutil from gitlab (currently doesn't work, git and cygwin don't play nice,...
   # TODO: ...because one is Unix, ond is Windows).

pyramid/diagnostics.py

@@ -492,7 +492,7 @@ class LCurve(object):
         self.chisq_m = []
         if save_dir is not None:
             assert os.path.isdir(save_dir), 'save_dir has to be None or a valid directory!'
-        self.save_dir = save_dir
+        self.save_dir = save_dir  # TODO: Use save_dir!!!
         self._log.debug('Created ' + str(self))
 
     def calculate(self, lam):

pyramid/fielddata.py

@@ -794,6 +794,9 @@ class VectorData(FieldData):
         from .file_io.io_vectordata import save_vectordata
         save_vectordata(self, filename, **kwargs)
 
+    # TODO: we have 2D and 3D plots, what about 1D line of vector arrows? Would be nice!
+    # TODO: Make all a bit more flexible with squeeze (so dimensions are not as strict).
+
     def plot_quiver(self, ar_dens=1, log=False, scaled=True, scale=1., b_0=None, qkey_unit='T',
                     coloring='angle', cmap=None,  # Used here and plot_streamlines!
                     proj_axis='z', ax_slice=None, show_mask=True, bgcolor=None, axis=None,

pyramid/forwardmodel.py

@@ -375,6 +375,7 @@ class DistributedForwardModel(ForwardModel):
         self.proc_hook_points = [0]
         self.pipes = []
         self.processes = []
+        print('NPROCS:', self.nprocs)    # TODO: Logging instead of printing!
         for proc_id in range(self.nprocs):
             # Create SubDataSets:
             sub_data = DataSet(self.data_set.a, self.data_set.dim, self.data_set.b_0,
@@ -510,6 +511,7 @@ class DistributedForwardModel(ForwardModel):
 
 def _worker(fwd_model, pipe):
     # Has to be directly accessible in the module as a function, NOT a method of a class instance!
+    # TODO: Logging instead of printing!
     print('... {} starting!'.format(mp.current_process().name))
     sys.stdout.flush()
     for method, arguments in iter(pipe.recv, 'STOP'):

pyramid/phasemap.py

@@ -31,6 +31,8 @@ from . import plottools
 __all__ = ['PhaseMap']
 
 
+# TODO: check out pint for units and stuff!
+
 class PhaseMap(object):
     """Class for storing phase map data.
 

pyramid/regularisator.py

@@ -18,7 +18,7 @@ __all__ = ['NoneRegularisator', 'ZeroOrderRegularisator', 'FirstOrderRegularisat
            'ComboRegularisator']
 
 
-class Regularisator(object, metaclass=abc.ABCMeta):
+class Regularisator(object, metaclass=abc.ABCMeta):  # TODO: Does this have to be abstract??
     """Class for providing a regularisation term which implements additional constraints.
 
     Represents a certain constraint for the 3D magnetization distribution whose cost is to minimize

pyramid/utils/reconstruction_2d_from_phasemap.py

@@ -45,7 +45,7 @@ def reconstruction_2d_from_phasemap(phasemap, b_0=1, lam=1E-3, max_iter=100, ram
         If True, the results are plotted after reconstruction.
     ar_dens: int, optional
         Number defining the arrow density which is plotted. A higher ar_dens number skips more
-        arrows (a number of 2 plots every second arrow). Default is 1.
+        arrows (a number of 2 plots every second arrow). Will be estimated if not provided.
     verbose: bool, optional
         If set to True, information like a progressbar is displayed during reconstruction.
         The default is False.

pyramid/utils/reconstruction_3d_from_magdata.py

@@ -10,6 +10,8 @@ import numpy as np
 
 import multiprocessing as mp
 
+from jutil.taketime import TakeTime
+
 from .. import reconstruction
 from ..dataset import DataSet
 from ..projector import XTiltProjector, YTiltProjector

pyramid/version.py

 # -*- coding: utf-8 -*-
 """"This file is generated automatically by the Pyramid `setup.py`"""
-version = "0.1.0-dev"
+version = "0.1.0.dev0"
 hg_revision = "???"