Merge pull request #321 from jadball/multiphase

Support for extended data analysis parameters

ImageD11/parameters.py

@@ -1 +1,310 @@
-from xfab.parameters import *
+# temporary comment out for new pars development:
+# from xfab.parameters import *
+
+from __future__ import print_function
+
+# ImageD11_v0.4 Software for beamline ID11
+# Copyright (C) 2005  Jon Wright
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+# Moved from ImageD11 to xfab 07/11/2019
+
+"""
+Class to handle groups of parameters to be saved in and out
+of files and edited in guis with the fixed/varied info etc
+"""
+
+
+from xfab import xfab_logging
+
+logger = xfab_logging.get_module_level_logger(__name__)
+
+
+class AnalysisSchema:
+    """Class to handle more complicated data analysis parameters."""
+
+    def __init__(self, filename=None):
+        # the dictionary of everything we found from file
+        self.pars_dict = dict()
+
+        # a parameters object for the geometry
+        self.geometry_pars_obj = None
+
+        # a dict of parameters object for each phase
+        self.phase_pars_obj_dict = dict()
+
+        if filename is not None:
+            self.load_json(filename)
+            self.get_pars_objects()
+
+    def get_pars_objects(self):
+        """Parses self.pars_dict, reads the .par files, makes parameter objects for them"""
+        # get geometric parameters
+        geometry_dict = self.pars_dict["geometry"]
+        geometry_file = geometry_dict["file"]
+        self.geometry_pars_obj = parameters()
+        self.geometry_pars_obj.loadparameters(geometry_file)
+
+        # get phase parameters from one of the phases
+        phases_dict = self.pars_dict["phases"]
+        for phase_name, phase_entry in phases_dict.items():
+            phase_file = phase_entry["file"]
+            # read the phase pars from disk
+            phase_pars_obj = parameters()
+            phase_pars_obj.loadparameters(phase_file)
+            # put this pars object in self.phase_pars_obj_dict
+            self.phase_pars_obj_dict[phase_name] = phase_pars_obj
+
+    def get_any_phase_pars_obj(self):
+        """Returns any parameters object from self.phase_pars_obj_dict"""
+        return next(iter(self.phase_pars_obj_dict.values()))
+
+    @property
+    def xfab_pars_dict(self):
+        """Build a xfab pars compatible dictionary"""
+        # get geometry pars as a dict
+        geometry_pars_dict = self.geometry_pars_obj.get_parameters()
+        # get any phase pars as a dict
+        phase_pars_dict = self.get_any_phase_pars_obj().get_parameters()
+        # combine dicts together
+        pars_dict = phase_pars_dict.copy()
+        pars_dict.update(geometry_pars_dict)
+        return pars_dict
+
+    def load_json(self, filename):
+        """
+        Load json from file
+        """
+        import json
+        with open(filename, 'r') as json_string:
+            self.pars_dict = json.load(json_string)
+
+
+class par:
+    """
+    Represents a thing which can vary
+    """
+
+    def __init__(self, name, value, helpstring=None,
+                 vary=False, can_vary=False, stepsize=None):
+        """
+        name : unique key used as keyword arg to some functions
+        value : value of the parameter
+        helpstring : optional string to help user
+        vary : value should be optimised
+        can_vary : value is not fixed
+        stepsize : guessestimated ball park step size (eg not 1e99!)
+        """
+        self.name = name
+        self.value = value
+        if helpstring is None:
+            self.helpstring = "parameter : " + name
+        else:
+            self.helpstring = helpstring
+        self.vary = vary
+        self.can_vary = can_vary
+        self.stepsize = stepsize
+
+    def fromstringlist(self, sl):
+        """ to send to Java """
+        [self.name,
+         self.value,
+         self.helpstring,
+         self.vary,
+         self.can_vary,
+         self.stepsize] = sl
+
+    def tostringlist(self):
+        """ to catch from Java """
+        return [self.name,
+                self.value,
+                self.helpstring,
+                self.vary,
+                self.can_vary,
+                self.stepsize]
+
+
+class parameters:
+    """
+    Class to hold a set of named parameters
+    """
+
+    def __init__(self, **kwds):
+        """
+        name=value style arg list
+        """
+        self.parameters = kwds
+        self.varylist = []
+        self.can_vary = {}
+        self.variable_list = []
+        self.stepsizes = {}
+        self.par_objs = {}
+        for k, v in list(self.parameters.items()):
+            self.addpar(par(k, v))
+
+    def addpar(self, par):
+        """
+        add a parameter object
+        """
+        self.parameters[par.name] = par.value
+        self.can_vary[par.name] = par.can_vary
+        if par.vary and par.name not in self.varylist:
+            self.varylist.append(par.name)
+        if par.can_vary and par.name not in self.variable_list:
+            self.variable_list.append(par.name)
+            self.stepsizes[par.name] = par.stepsize
+        self.par_objs[par.name] = par
+
+    def get_variable_list(self):
+        return self.variable_list
+
+    def get_variable_values(self):
+        """ values of the parameters """
+        return [self.parameters[name] for name in self.varylist]
+
+    def get_variable_stepsizes(self):
+        """ stepsizes for optimisers """
+        return [self.stepsizes[name] for name in self.varylist]
+
+    def set_varylist(self, vl):
+        ks = list(self.parameters.keys())
+        for v in vl:
+            assert v in ks
+            assert v in self.variable_list
+        self.varylist = vl
+
+    def set_variable_values(self, values):
+        """ set values of the parameters"""
+        assert len(values) == len(self.varylist)
+        for name, value in zip(self.varylist, values):
+            self.parameters[name] = value
+
+    def set_parameters(self, d):
+        """
+        Updates the values of parameters
+        """
+        self.parameters.update(d)
+        self.dumbtypecheck()
+
+    def get_parameters(self):
+        """
+        Returns a dictionary of parameters
+        """
+        return self.parameters
+
+    def get(self, name):
+        return self.parameters[name]
+
+    def set(self, name, value):
+        self.parameters[name] = value
+
+    def update_yourself(self, other):
+        """
+        Sychronise this parameter objects list of values with another object
+        """
+        for k, v in list(self.parameters.items()):
+            if hasattr(other, k):
+                var = getattr(other, k)
+                logger.debug("setting: pars[%s] from %s to %s" % (k, v, var))
+                self.parameters[k] = var
+            else:
+                logger.debug("error: %s has no attribute %s, ignoring" % (other, k))
+
+    def update_other(self, other):
+        """
+        Synchronise an object with the values in this object
+        """
+        for k, v in list(self.parameters.items()):
+            if hasattr(other, k):
+                var = getattr(other, k)
+                logger.debug("setting: %s.%s from %s to %s" % (other, k, var, v))
+                setattr(other, k, v)
+            else:
+                logger.debug("error: %s has no attribute %s, ignoring" %
+                             (other, k))
+
+    def saveparameters(self, filename):
+        """
+        Write parameters to a file
+        """
+        f = open(filename, "w")
+        keys = list(self.parameters.keys())
+        keys.sort()
+        for key in keys:
+            f.write("%s %s\n" % (key, str(self.parameters[key])))
+        f.close()
+
+    def loadparameters(self, filename):
+        """
+        Load parameters from a file
+        """
+        # is it a json file?
+        if filename.endswith('json'):
+            # create a JsonPars object and get the pars dict from it
+            pars_dict = AnalysisSchema(filename=filename).xfab_pars_dict
+            self.parameters.update(pars_dict)
+        else:
+            lines = open(filename, "r").readlines()
+            for line in lines:
+                try:
+                    [name, value] = line.split(" ")
+                    name = name.replace("-", "_")
+                    self.parameters[name] = value
+                except ValueError:
+                    logger.error("Failed to read:%s" % (line))
+        self.dumbtypecheck()
+
+    def dumbtypecheck(self):
+        """
+        Eventually parameter types (and units and fixed/varied to be
+        specifieable
+        For now it just tries to coerce to float, then does nothing
+        """
+        for name, value in list(self.parameters.items()):
+            if type(value) == type("string"):
+                try:
+                    vf = float(value)
+                except ValueError:
+                    # it really is a string
+                    self.parameters[name] = value.lstrip().rstrip()
+                    continue
+                # here if float worked
+                try:
+                    vi = int(value)
+                except ValueError:
+                    # it really is a float
+                    self.parameters[name] = vf
+                    continue
+
+                # here if float and int worked
+                # should not be needed, depends on int valueerror
+                if abs(vi - vf) < 1e-9:
+                    # use int
+                    self.parameters[name] = vi
+                    continue
+                else:
+                    self.parameters[name] = vf
+                    continue
+            else:
+                # int/float preserve type
+                self.parameters[name] = value
+
+
+def read_par_file(filename):
+    p = parameters()
+    p.loadparameters(filename)
+    return p
+

ImageD11/unitcell.py

@@ -33,6 +33,7 @@
 from ImageD11 import cImageD11
 from xfab import tools
 from scipy.spatial.transform import Rotation as ScipyRotation
+from ImageD11.parameters import AnalysisSchema
 
 
 def radians(x):
@@ -158,6 +159,24 @@ def cellfromstring(s):
     return unitcell(latt, symm)
 
 
+class Phases(AnalysisSchema):
+    """
+    Phases class - extends AnalysisSchema from xfab.parameters
+    Reads analysis parameters from file
+    Contains self.unitcells which is a dict of unitcell objects
+    """
+    def __init__(self, filename):
+        super(Phases, self).__init__(filename)
+        self.unitcells = {}
+        if filename is not None:
+            self.get_unitcells()
+
+    def get_unitcells(self):
+        # dict of parameter objects for each phase
+        for phase_name, phase_pars_obj in self.phase_pars_obj_dict.items():
+            self.unitcells[phase_name] = unitcell_from_parameters(phase_pars_obj)
+
+
 class unitcell:
     # Unit cell stuff
     # Generate a list of peaks from a unit cell