Rename Fit variables consistently, cleanup

Author: Lemonexe

appPy/cli/fit.py

@@ -17,7 +17,7 @@
 @click.command()
 @click.argument('compound1')
 @click.argument('compound2')
-@click.option('-m', '--model', help=f'Which model to fit, enter one of: {model_list}')
+@click.argument('model')
 @click.option('-d', '--datasets', help='Comma-separated exact dataset names, otherwise do all datasets of the system')
 @click.option('-p', '--params', help='Comma-separated initial parameters, will ignore params saved in file')
 @click.option('-c', '--consts', help='Comma-separated names of parameters to be kept constant')

appPy/src/fit/Fit.py

@@ -15,24 +15,16 @@ def __init__(self, supported_models, model_name, params0, const_param_names=None
         const_param_names (list of str): names of parameter names to be kept constant during optimization.
         """
         super().__init__()
-        self.keys_to_serialize = [
-            'is_optimized', 'nparams', 'nparams0', 'RMS_init', 'RMS_final', 'AAD_init', 'AAD_final'
-        ]
+        self.keys_to_serialize = ['nparams0', 'RMS0', 'AAD0']
         self.supported_models = supported_models
-        self.is_optimized = False  # whether optimization has been performed
 
         self.model = get_model_by_name(supported_models, model_name)
         self.params0, self.nparams0 = self.__parse_params0(params0)  # initial params as np.array, and as dict
-        self.params = self.params0  # optimization result params as np.array
-        self.nparams = self.nparams0
 
         self.const_param_names = self.__parse_const_param_names(const_param_names)
 
-        # initial and final objective function values
-        self.RMS_init = None
-        self.AAD_init = None
-        self.RMS_final = None
-        self.AAD_final = None
+        # initial objective function values
+        self.RMS0 = self.AAD0 = None
 
     def set_named_params(self, params):
         """Compose vector of ordered params into an ordered dict of named params."""
@@ -44,12 +36,12 @@ def __parse_params0(self, params0):
         params0: either ordered list of float, or named params as ordered key:value dict
         """
         model = self.model
-        if not params0: return model.params0, dict(zip(model.param_names, model.params0))
+        if not params0: return model.params0, self.set_named_params(model.params0)
         if isinstance(params0, dict):
             nparams0 = params0
             params0 = [params0[key] for key in model.param_names]
         else:
-            nparams0 = dict(zip(model.param_names, params0))
+            nparams0 = self.set_named_params(params0)
         if len(params0) != model.n_params:
             raise AppException(f'{model.display_name} model expects {model.n_params} parameters, got {len(params0)}!')
         return params0, nparams0

appPy/src/fit/Fit_VLE.py

@@ -27,7 +27,7 @@ def __init__(self, compound1, compound2, model_name, datasets, params0, const_pa
         const_param_names (list of str): names of parameters to be kept constant during optimization.
         """
         super().__init__(supported_models, model_name, params0, const_param_names)
-        self.keys_to_serialize.extend(['tabulated_datasets'])
+        self.keys_to_serialize.extend(['is_optimized', 'tabulated_datasets', 'nparams', 'RMS_final', 'AAD_final'])
         self.compound1 = compound1
         self.compound2 = compound2
 
@@ -43,8 +43,13 @@ def __init__(self, compound1, compound2, model_name, datasets, params0, const_pa
         self.gamma_1 = squash(self.dataset_VLEs, 'gamma_1')
         self.gamma_2 = squash(self.dataset_VLEs, 'gamma_2')
 
-        self.RMS_init = RMS(self.get_residual(self.params0))
-        self.AAD_init = AAD(self.get_residual(self.params0))
+        self.params = self.params0  # optimization result params as np.array
+        self.nparams = self.nparams0
+
+        self.is_optimized = False  # whether optimization has been performed
+        self.RMS_final = self.AAD_final = None
+        self.RMS0 = RMS(self.get_residual(self.params0))
+        self.AAD0 = AAD(self.get_residual(self.params0))
 
     def __check_model_suitability(self):
         """Check if the model is appropriate for given datasets."""
@@ -88,8 +93,8 @@ def report(self):
             echo(f'  {name} = {value:.4g}')
 
         echo('')
-        echo(f'Initial RMS = {self.RMS_init:.3g}')
-        echo(f'Initial AAD = {self.AAD_init:.3g}')
+        echo(f'Initial RMS = {self.RMS0:.3g}')
+        echo(f'Initial AAD = {self.AAD0:.3g}')
         if self.is_optimized:
             echo(f'Final RMS   = {self.RMS_final:.3g}')
             echo(f'Final AAD   = {self.AAD_final:.3g}')

appPy/src/fit/Fit_Vapor.py

@@ -20,27 +20,28 @@ def __init__(self, compound, model_name, p_data, T_data, params0):
         p_data (list of float): vector of pressure data.
         T_data (list of float): vector of temperature data.
         params0 (list of float): initial estimate of model parameters (ordered).
-        skip_T_p_optimization (bool): if True, only p residuals will be optimized.
         """
         super().__init__(supported_models, model_name, params0)
-        self.keys_to_serialize.extend(
-            ['is_T_p_optimized', 'odr_messages', 'RMS_inter', 'AAD_inter', 'nparams_inter', 'T_min', 'T_max'])
+        self.keys_to_serialize.extend([
+            'is_p_optimized', 'is_T_p_optimized', 'odr_messages', 'nparams_p', 'nparams_T_p', 'RMS_p', 'AAD_p',
+            'RMS_T_p', 'AAD_T_p', 'T_min', 'T_max'
+        ])
         self.compound = compound
         self.p_data = np.array(p_data)
         self.T_data = np.array(T_data)
         # will be offered as model T_min & T_max
         self.T_min = np.min(T_data)
         self.T_max = np.max(T_data)
 
-        self.T_tab = self.p_tab_inter = self.p_tab_final = None
-        self.nparams_inter = self.params_inter = None
-        self.RMS_inter = self.AAD_inter = None
-        self.is_T_p_optimized = False  # in case of Fit_Vapor, Fit.is_optimized means is_p_optimized
+        self.nparams_p = self.params_p = self.params_T_p = self.nparams_T_p = None
+        self.RMS_p = self.AAD_p = self.RMS_T_p = self.AAD_T_p = None
+        self.T_tab = self.p_tab_p = self.p_tab_T_p = None
+        self.is_p_optimized = self.is_T_p_optimized = False
         self.odr_messages = []  # scipy.ODR has an unusual output format, as array of messages, but no status
 
         # even for ODR, only p residuals are calculated for simplicity, so they may actually increase after ODR
-        self.RMS_init = RMS(self.get_p_residuals(self.params0))
-        self.AAD_init = AAD(self.get_p_residuals(self.params0))
+        self.RMS0 = RMS(self.get_p_residuals(self.params0))
+        self.AAD0 = AAD(self.get_p_residuals(self.params0))
 
     def get_p_residuals(self, params):
         """With given params, calculate residuals only of the dependent variable (p)."""
@@ -55,15 +56,15 @@ def optimize_p(self):
         if result.status <= 0:
             self.warn(f'p-optimization failed! Status {result.status}: {result.message}')
             return
-        self.is_optimized = True
-        self.params_inter = merge_params(result.x)
-        self.nparams_inter = self.set_named_params(self.params_inter)
-        self.RMS_inter = RMS(self.get_p_residuals(self.params_inter))
-        self.AAD_inter = AAD(self.get_p_residuals(self.params_inter))
+        self.is_p_optimized = True
+        self.params_p = merge_params(result.x)
+        self.nparams_p = self.set_named_params(self.params_p)
+        self.RMS_p = RMS(self.get_p_residuals(self.params_p))
+        self.AAD_p = AAD(self.get_p_residuals(self.params_p))
 
     def optimize_T_p(self):
         """Optimize the model params, considering errors of both dependent (p) & independent (T) variables."""
-        full_params0 = self.params_inter if self.is_optimized else self.params  # use intermediate params if available
+        full_params0 = self.params_p if self.is_p_optimized else self.params0  # use intermediate params if available
         fun2wrap = lambda params, x: self.model.fun(x, *params)  # swap the order of params and x
         var_params0, wrapped_fun, merge_params = const_param_wrappers(fun2wrap, full_params0, self.const_param_names,
                                                                       self.model.param_names)
@@ -76,19 +77,19 @@ def optimize_T_p(self):
             self.warn(f'T,p-optimization failed with error: {e}')
             return
         self.is_T_p_optimized = True
-        self.params = merge_params(odr_result.beta)
-        self.nparams = self.set_named_params(self.params)
-        self.RMS_final = RMS(self.get_p_residuals(self.params))
-        self.AAD_final = AAD(self.get_p_residuals(self.params))
+        self.params_T_p = merge_params(odr_result.beta)
+        self.nparams_T_p = self.set_named_params(self.params_T_p)
+        self.RMS_T_p = RMS(self.get_p_residuals(self.params_T_p))
+        self.AAD_T_p = AAD(self.get_p_residuals(self.params_T_p))
         self.odr_messages = odr_result.stopreason
         self.odr_messages = self.odr_messages if isinstance(self.odr_messages, list) else [self.odr_messages]
 
     def tabulate(self):
         self.T_tab = np.linspace(self.T_min, self.T_max, cst.x_points_smooth_plot)
-        if self.is_optimized:
-            self.p_tab_inter = self.model.fun(self.T_tab, *self.params_inter)
+        if self.is_p_optimized:
+            self.p_tab_p = self.model.fun(self.T_tab, *self.params_p)
         if self.is_T_p_optimized:
-            self.p_tab_final = self.model.fun(self.T_tab, *self.params)
+            self.p_tab_T_p = self.model.fun(self.T_tab, *self.params_T_p)
 
     def report(self):
         underline_echo(self.get_title())
@@ -98,14 +99,14 @@ def report(self):
         echo('')
 
         echo('Optimized parameters as intermediate & final value:')
-        for (name, p_inter, p_final) in zip(self.model.param_names, self.params_inter, self.params):
-            echo(f'  {name} = {p_inter:7.4g} {p_final:9.4g}')
+        for (name, p_p, p_T_p) in zip(self.model.param_names, self.params_p, self.params_T_p):
+            echo(f'  {name} = {p_p:7.4g} {p_T_p:9.4g}')
 
         echo('')
-        echo(f'Initial RMS = {self.RMS_init:.3g}')
-        echo(f'Initial AAD = {self.AAD_init:.3g}')
-        echo(f'Final RMS   = {self.RMS_final:.3g}')
-        echo(f'Final AAD   = {self.AAD_final:.3g}')
+        echo(f'Initial RMS = {self.RMS0:.3g}')
+        echo(f'Initial AAD = {self.AAD0:.3g}')
+        echo(f'Final RMS   = {self.RMS_T_p:.3g}')
+        echo(f'Final AAD   = {self.AAD_T_p:.3g}')
 
     def get_title(self):
         return f'Regression of {self.model.display_name} on {self.compound}'

appPy/src/plot/Fit_Vapor_plot.py

@@ -20,13 +20,13 @@ def decorate(self):
 
     def plot_p(self, mode):
         """Overlay p-fitted model over vapor pressure data."""
-        if not self.is_optimized: return None
+        if not self.is_p_optimized: return None
         init_plot(mode)
         self.draw_data()
 
         T_tab_disp = convert_T(self.T_tab)
-        p_tab_inter_disp = convert_p(self.p_tab_inter)
-        plt.plot(T_tab_disp, p_tab_inter_disp, '-k', label='p-fitted model')
+        p_tab_p_disp = convert_p(self.p_tab_p)
+        plt.plot(T_tab_disp, p_tab_p_disp, '-k', label='p-fitted model')
 
         self.decorate()
         return finish_plot(mode)
@@ -38,8 +38,8 @@ def plot_T_p(self, mode):
         self.draw_data()
 
         T_tab_disp = convert_T(self.T_tab)
-        p_tab_final_disp = convert_p(self.p_tab_final)
-        plt.plot(T_tab_disp, p_tab_final_disp, '-k', label='T,p-fitted model')
+        p_tab_T_p_disp = convert_p(self.p_tab_T_p)
+        plt.plot(T_tab_disp, p_tab_T_p_disp, '-k', label='T,p-fitted model')
 
         self.decorate()
         return finish_plot(mode)

appUI/src/actions/FitVLE/FitVLEResultsDialog.tsx

@@ -50,7 +50,7 @@ export const FitVLEResultsDialog: FC<FitResultsDialogProps> = ({ open, handleClo
     }, [data]);
 
     const metricsSpreadsheetData = useMemo(() => {
-        const rows = [[data.RMS_init, data.AAD_init]];
+        const rows = [[data.RMS0, data.AAD0]];
         if (optimized) rows.push([data.RMS_final!, data.AAD_final!]);
         return makeReadOnly(spreadsheetToSigDgts(matrixToSpreadsheetData(rows), sigDgtsMetrics));
     }, [data]);

appUI/src/actions/FitVapor/FitVaporResultsDialog.tsx

@@ -34,12 +34,12 @@ export const FitVaporResultsDialog: FC<FitVaporResultsDialogProps> = ({
 }) => {
     const [infoOpen, setInfoOpen] = useState(false);
 
-    const optimizedP = data.is_optimized;
+    const optimizedP = data.is_p_optimized;
     const optimizedTP = data.is_T_p_optimized;
     const paramNames = useMemo(() => fromNamedParams(data.nparams0)[0], [data]);
     const params0 = fromNamedParams(data.nparams0)[1];
-    const paramsP = fromNamedParams(data.nparams_inter)[1];
-    const paramsTP = fromNamedParams(data.nparams)[1];
+    const paramsP = fromNamedParams(data.nparams_p)[1];
+    const paramsTP = fromNamedParams(data.nparams_T_p)[1];
 
     const rowLabels = useMemo(() => {
         const rows = ['initial'];
@@ -49,9 +49,9 @@ export const FitVaporResultsDialog: FC<FitVaporResultsDialogProps> = ({
     }, [data]);
 
     const metricsSpreadsheetData = useMemo(() => {
-        const rows = [[data.RMS_init, data.AAD_init]];
-        if (optimizedP) rows.push([data.RMS_inter!, data.AAD_inter!]);
-        if (optimizedTP) rows.push([data.RMS_final!, data.AAD_final!]);
+        const rows = [[data.RMS0, data.AAD0]];
+        if (optimizedP) rows.push([data.RMS_p!, data.AAD_p!]);
+        if (optimizedTP) rows.push([data.RMS_T_p!, data.AAD_T_p!]);
         return makeReadOnly(spreadsheetToSigDgts(matrixToSpreadsheetData(rows), sigDgtsMetrics));
     }, [data]);
 

appUI/src/adapters/api/types/fitTypes.ts

@@ -44,18 +44,17 @@ export type PlottedDataset = AnalysisResult & {
     gamma_plot: string;
 };
 
-type FitMetrics = AnalysisResult & {
+export type FitAnalysisResponse = AnalysisResult & {
     is_optimized: boolean;
-    RMS_init: number;
-    RMS_final: number | null;
-    AAD_init: number;
-    AAD_final: number | null;
-};
+    tabulated_datasets: PlottedDataset[];
 
-export type FitAnalysisResponse = FitMetrics & {
     nparams0: NamedParams;
     nparams: NamedParams;
-    tabulated_datasets: PlottedDataset[];
+
+    RMS0: number;
+    RMS_final: number | null;
+    AAD0: number;
+    AAD_final: number | null;
 };
 
 export type FitTabulateRequest = SystemIdentifier & { model_name: string; p: number };
@@ -77,7 +76,7 @@ export type VaporFitRequest = CompoundIdentifier & {
 };
 
 export type VaporFitResponse = AnalysisResult & {
-    is_optimized: boolean;
+    is_p_optimized: boolean;
     is_T_p_optimized: boolean;
     odr_messages: string[];
     T_min: number;
@@ -86,13 +85,13 @@ export type VaporFitResponse = AnalysisResult & {
     plot_T_p?: string;
 
     nparams0: NamedParams;
-    nparams_inter?: NamedParams;
-    nparams?: NamedParams;
+    nparams_p?: NamedParams;
+    nparams_T_p?: NamedParams;
 
-    RMS_init: number;
-    RMS_inter: number | null;
-    RMS_final: number | null;
-    AAD_init: number;
-    AAD_inter: number | null;
-    AAD_final: number | null;
+    RMS0: number;
+    RMS_p: number | null;
+    RMS_T_p: number | null;
+    AAD0: number;
+    AAD_p: number | null;
+    AAD_T_p: number | null;
 };

dev/notes_VLizard.txt

@@ -55,11 +55,11 @@ pipenv run cli\gamma CHF CHOL -d 25kPa --plot
 pipenv run cli\rk CHF CHOL -d 25kPa,40kPa --plot
 pipenv run cli\herington CHF CHOL -d 25kPa,40kPa
 pipenv run cli\fredenslund CHF CHOL -d 25kPa --ge --res
-pipenv run cli\fit CPF CPOL -m vanLaar -d 25kPa --txy --persist
+pipenv run cli\fit CPF CPOL vanLaar -d 25kPa --txy --persist
 pipenv run cli\tabulate CPOL CPF vanLaar 33 --txy
 pipenv run cli\vn CPOL CPF vanLaar -d 25kPa --plot
-pipenv run cli\fit CHOL CHF -d 10kPa,25kPa,40kPa --xy --txy --gamma -c c_12
-pipenv run cli\fit EtOH H2O -m UNIQUAC --skip -d Kamihama2012,Voutsas2011 --xy --gamma -p 1.972,1.4,2.10547,0.92,2.0046,-2.4936,-728.9705,756.9477
+pipenv run cli\fit CHOL CHF NRTL -d 10kPa,25kPa,40kPa --xy --txy --gamma -c c_12
+pipenv run cli\fit EtOH H2O UNIQUAC --skip -d Kamihama2012,Voutsas2011 --xy --gamma -p 1.972,1.4,2.10547,0.92,2.0046,-2.4936,-728.9705,756.9477
 ```
 See [appPy/cli](../appPy/cli), where filenames correspond to commands;
 calling with `--help` will instruct you further.

docs/appPy.md

@@ -7,7 +7,7 @@ Accept: application/json
 POST http://localhost:37137/fit/vle
 Content-Type: application/json
 
-{"compound1": "EtOH", "compound2": "H2O", "model_name": "vanLaar", "datasets":  ["1939vac"],
+{"compound1": "EtOH", "compound2": "H2O", "model_name": "vanLaar", "datasets":  ["Voutsas2011"],
   "skip_optimization": false, "nparams0": {"A_12": 0.4, "A_21": 0.1}}
 
 ###
@@ -35,8 +35,7 @@ Content-Type: application/json
   "model_name": "Wagner",
   "p_data": [9.98, 11.52, 14.39, 25.01, 25.95, 39.91, 40.05, 52.5, 60.41, 78.21, 89.63, 100.05],
   "T_data": [363.95, 367.65, 373.55, 389.25, 390.25, 403.35, 403.55, 412.45, 417.15, 426.25, 431.25, 435.35],
-  "nparams0": {"A": -7.898313, "B": 1.997515, "C": -2.448405, "D": -1.880206, "T_c": 647, "p_c": 22071},
-  "skip_T_p_optimization": false
+  "nparams0": {"A": -7.898313, "B": 1.997515, "C": -2.448405, "D": -1.880206, "T_c": 647, "p_c": 22071}
 }
 
 ###