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Adds conversion between R1 .mat files and Python Projects (#55)
* working r1-to-rat converter and tests * adds project class to r1 converter * project to r1 now functional * fixed various issues - tests all now pass * added scipy to setup.py and requirements * added test data * removed errant comment * removed case sensitivity workaround * added conversion tutorial * review fixes and tutorials added * set to skip for now * review fixes * added Python custom file * review fixes * fixed circular import
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‎RATapi/__init__.py‎

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from RATapi.controls import Controls
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from RATapi.project import Project
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from RATapi.run import run
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from RATapi.utils import plotting
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from RATapi.utils import convert, plotting
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__all__ = ["examples", "models", "events", "ClassList", "Controls", "Project", "run", "plotting"]
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__all__ = ["examples", "models", "events", "ClassList", "Controls", "Project", "run", "plotting", "convert"]

‎RATapi/examples/__init__.py‎

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from RATapi.examples.absorption.absorption import absorption
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from RATapi.examples.convert_rascal_project import convert_rascal
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from RATapi.examples.domains.domains_custom_layers import domains_custom_layers
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from RATapi.examples.domains.domains_custom_XY import domains_custom_XY
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from RATapi.examples.domains.domains_standard_layers import domains_standard_layers
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"DSPC_custom_layers",
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"DSPC_custom_XY",
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"DSPC_standard_layers",
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"convert_rascal",
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]

‎RATapi/examples/convert_rascal_project/Model_IIb.m‎

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function [output,sub_rough] = Model_IIb(params,bulk_in,bulk_out,contrast)
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%MODEL_1 RASCAL Custom Layer Model File.
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%
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%
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% This file accepts 3 vectors containing the values for
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% Params, bulk in and bulk out
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% The final parameter is an index of the contrast being calculated
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% The m-file should output a matrix of layer values, in the form..
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% Output = [thick 1, SLD 1, Rough 1, Percent Hydration 1, Hydrate how 1
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% ....
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% thick n, SLD n, Rough n, Percent Hydration n, Hydration how n]
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% The "hydrate how" parameter decides if the layer is hydrated with
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% Bulk out or Bulk in phases. Set to 1 for Bulk out, zero for Bulk in.
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% Alternatively, leave out hydration and just return..
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% Output = [thick 1, SLD 1, Rough 1,
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% ....
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% thick n, SLD n, Rough n] };
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% The second output parameter should be the substrate roughness
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Roughness = params(1);
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APM = params(2);
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thickHead = params(3);
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theta = params(4);
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% vTail = params(4);
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% vHead = params(5);
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%Make a flag to say which deuteration this is calculating
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%[subs head tail]
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deut = [0 0 1;
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1 0 1;
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0 1 0;
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1 1 0;
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0 1 1;
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1 1 1;
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1 0 0];
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%Neutron b's..
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%define all the neutron b's.
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bc = 0.6646e-4; %Carbon
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bo = 0.5843e-4; %Oxygen
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bh = -0.3739e-4; %Hydrogen
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bp = 0.513e-4; %Phosphorus
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bn = 0.936e-4; %Nitrogen
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bd = 0.6671e-4; %Deuterium
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%Work out the total scattering length in each fragment....
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%Define scattering lengths..
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%Hydrogenated version....
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COO = (4*bo) + (2*bc);
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GLYC = (3*bc) + (5*bh);
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CH3 = (2*bc) + (6*bh);
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PO4 = (1*bp) + (4*bo);
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CH2 = (1*bc) + (2*bh);
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CHOL = (5*bc) + (12*bh) + (1*bn);
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H2O = (2*bh) + (1*bo);
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%..and deuterated...
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dGLYC = (3*bc) + (5*bd);
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dCH3 = (2*bc) + (6*bd);
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dCH2 = (1*bc) + (2*bd);
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dCHOL = (5*bc) + (12*bd) + (1*bn);
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D2O = (2*bd) + (1*bo);
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%And also volumes....
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vCH3 = 52.7;
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vCH2 = 28.1;
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vCOO = 39.0;
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vGLYC = 68.8;
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vPO4 = 53.7;
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vCHOL = 120.4;
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vWAT = 30.4;
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vHead = vCHOL + vPO4 + vGLYC + 2*vCOO;
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vTail = 2*(16*vCH2)+ 2*(vCH3);
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%Make the SLD's first...
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thisMask = deut(contrast,:);
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switch thisMask(1)
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case 0
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thisWater = (H2O * 0.9249) + (D2O * 0.0871);
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case 1
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thisWater = D2O;
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end
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%Calculate mole fraction of D2O from the bulk SLD..
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d2o_molfr = (1/D2O-H2O)*((bulk_out(contrast)/0.036182336306)-H2O);
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thisWater = (d2o_molfr * D2O) + ((1-d2o_molfr)*H2O);
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switch thisMask(2)
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case 0
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thisHead = CHOL + PO4 + GLYC + COO;
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case 1
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thisHead = dCHOL + PO4 + GLYC + COO;
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end
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switch thisMask(3);
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case 0
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thisTail = (32*CH2) + CH3;
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case 1
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thisTail = (32*dCH2) + dCH3;
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end
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noWat = ((thickHead*APM)-vHead)/vWAT;
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thisHead = thisHead + noWat*thisWater;
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vHead = vHead + noWat*vWAT;
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sldHead = thisHead/vHead;
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%thickHead = vHead/APM;
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sldTail = thisTail/vTail;
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%thickTail = vTail/APM;
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thickTail = (1.5 + 16*1.265)*cosd(theta);
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output = [thickTail sldTail Roughness;
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thickHead sldHead Roughness;];
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sub_rough = Roughness;
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‎RATapi/examples/convert_rascal_project/Model_IIb.py‎

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from math import cos, radians
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def Model_IIb(params, bulk_in, bulk_out, contrast):
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# converted from matlab file Model_IIb.m
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Roughness, APM, thickHead, theta = params
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# Make a flag to say which deuteration this is calculating
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# [subs head tail]
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deut = [[0, 0, 1], [1, 0, 1], [0, 1, 0], [1, 1, 0], [0, 1, 1], [1, 1, 1], [1, 0, 0]]
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bc = 0.6646e-4 # Carbon
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bo = 0.5843e-4 # Oxygen
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bh = -0.3739e-4 # Hydrogen
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bp = 0.513e-4 # Phosphorus
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bn = 0.936e-4 # Nitrogen
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bd = 0.6671e-4 # Deuterium
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# Work out the total scattering length in each fragment
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# for hydrogenated:
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COO = (4 * bo) + (2 * bc)
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GLYC = (3 * bc) + (5 * bh)
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CH3 = (2 * bc) + (6 * bh)
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PO4 = (1 * bp) + (4 * bo)
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CH2 = (1 * bc) + (2 * bh)
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CHOL = (5 * bc) + (12 * bh) + (1 * bn)
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H2O = (2 * bh) + (1 * bo)
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# for deuterated:
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dCH3 = (2 * bc) + (6 * bd)
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dCH2 = (1 * bc) + (2 * bd)
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dCHOL = (5 * bc) + (12 * bd) + (1 * bn)
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D2O = (2 * bd) + (1 * bo)
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# for volumes:
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vCH3 = 52.7
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vCH2 = 28.1
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vCOO = 39.0
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vGLYC = 68.8
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vPO4 = 53.7
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vCHOL = 120.4
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vWAT = 30.4
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vHead = vCHOL + vPO4 + vGLYC + 2 * vCOO
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vTail = 2 * (16 * vCH2) + 2 * (vCH3)
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# make SLDs
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thisMask = deut[contrast]
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if thisMask[0] == 0:
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thisWater = (H2O * 0.9249) + (D2O * 0.0871)
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else:
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thisWater = D2O
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# Calculate mole fraction of D2O from the bulk SLD
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d2o_molfr = (1 / D2O - H2O) * ((bulk_out[contrast] / 0.036182336306) - H2O)
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thisWater = (d2o_molfr * D2O) + ((1 - d2o_molfr) * H2O)
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if thisMask[1] == 0:
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thisHead = CHOL + PO4 + GLYC + COO
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else:
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thisHead = dCHOL + PO4 + GLYC + COO
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if thisMask[2] == 0:
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thisTail = (32 * CH2) + CH3
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else:
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thisTail = (32 * dCH2) + dCH3
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noWat = ((thickHead * APM) - vHead) / vWAT
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thisHead = thisHead + noWat * thisWater
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vHead = vHead + noWat * vWAT
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sldHead = thisHead / vHead
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sldTail = thisTail / vTail
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thickTail = (1.5 + 16 * 1.265) * cos(radians(theta))
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output = [[thickTail, sldTail, Roughness], [thickHead, sldHead, Roughness]]
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sub_rough = Roughness
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return output, sub_rough

‎RATapi/examples/convert_rascal_project/R1monolayerVolumeModel.mat‎

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‎RATapi/examples/convert_rascal_project/__init__.py‎

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