[Equations] Fixes/rewrite to some operators, additional comments and …

…additional parsers (#828) ## Summary of Changes Fixes/rewrite to some operators — integral, summation, gradients Parser can handle: - Derivative has new enum component to identify various different notation. e.g. Leibniz, Newton, Euler, DNotation, Lagrange (Note that previous operator `PartialDerivative` is removed and partial derivative operator notation is now in `DerivativeNotation` enum. ) - Vector e.g. \vec{x} --------- Co-authored-by: Deepsana Shahi <[email protected]> Co-authored-by: Justin <[email protected]>
ml4ai · Feb 27, 2024 · 68e7d31 · 68e7d31
1 parent 2004566
commit 68e7d31
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diff --git a/skema/isa/data.py b/skema/isa/data.py
@@ -41,4 +41,4 @@
     </math>
     """
 
-expected = 'digraph G {\n0 [color=blue, label="Div(Γ*(H^(n+2))*(Abs(Grad(H))^(n-1))*Grad(H))"];\n1 [color=blue, label="D(1, t)(H)"];\n2 [color=blue, label="Γ*(H^(n+2))*(Abs(Grad(H))^(n-1))*Grad(H)"];\n3 [color=blue, label="Γ"];\n4 [color=blue, label="H^(n+2)"];\n5 [color=blue, label="H"];\n6 [color=blue, label="n+2"];\n7 [color=blue, label="n"];\n8 [color=blue, label="2"];\n9 [color=blue, label="Abs(Grad(H))^(n-1)"];\n10 [color=blue, label="Abs(Grad(H))"];\n11 [color=blue, label="Grad(H)"];\n12 [color=blue, label="n-1"];\n13 [color=blue, label="1"];\n1 -> 0  [color=blue, label="="];\n2 -> 0  [color=blue, label="Div"];\n3 -> 2  [color=blue, label="*"];\n4 -> 2  [color=blue, label="*"];\n5 -> 4  [color=blue, label="^"];\n6 -> 4  [color=blue, label="^"];\n7 -> 6  [color=blue, label="+"];\n8 -> 6  [color=blue, label="+"];\n9 -> 2  [color=blue, label="*"];\n10 -> 9  [color=blue, label="^"];\n11 -> 10  [color=blue, label="Abs"];\n5 -> 11  [color=blue, label="Grad"];\n12 -> 9  [color=blue, label="^"];\n7 -> 12  [color=blue, label="+"];\n13 -> 12  [color=blue, label="-"];\n11 -> 2  [color=blue, label="*"];\n}\n'
+expected = 'digraph G {\n0 [color=blue, label="Div(Γ*(H^(n+2))*(Abs(Grad(H))^(n-1))*Grad(H))"];\n1 [color=blue, label="PD(1, t)(H)"];\n2 [color=blue, label="Γ*(H^(n+2))*(Abs(Grad(H))^(n-1))*Grad(H)"];\n3 [color=blue, label="Γ"];\n4 [color=blue, label="H^(n+2)"];\n5 [color=blue, label="H"];\n6 [color=blue, label="n+2"];\n7 [color=blue, label="n"];\n8 [color=blue, label="2"];\n9 [color=blue, label="Abs(Grad(H))^(n-1)"];\n10 [color=blue, label="Abs(Grad(H))"];\n11 [color=blue, label="Grad(H)"];\n12 [color=blue, label="n-1"];\n13 [color=blue, label="1"];\n1 -> 0  [color=blue, label="="];\n2 -> 0  [color=blue, label="Div"];\n3 -> 2  [color=blue, label="*"];\n4 -> 2  [color=blue, label="*"];\n5 -> 4  [color=blue, label="^"];\n6 -> 4  [color=blue, label="^"];\n7 -> 6  [color=blue, label="+"];\n8 -> 6  [color=blue, label="+"];\n9 -> 2  [color=blue, label="*"];\n10 -> 9  [color=blue, label="^"];\n11 -> 10  [color=blue, label="Abs"];\n5 -> 11  [color=blue, label="Grad"];\n12 -> 9  [color=blue, label="^"];\n7 -> 12  [color=blue, label="+"];\n13 -> 12  [color=blue, label="-"];\n11 -> 2  [color=blue, label="*"];\n}\n'
diff --git a/skema/rest/tests/test_eqn_to_latex.py b/skema/rest/tests/test_eqn_to_latex.py
@@ -21,7 +21,7 @@ async def test_post_image_to_latex():
     # see https://fastapi.tiangolo.com/advanced/async-tests/#async-tests
     async with AsyncClient(app=app, base_url="http://eqn-to-latex-test") as ac:
         response = await ac.post(endpoint, files=files)
-    expected = "\\frac{d H}{dt}=\\nabla \\cdot {(\\Gamma*H^{n+2}*\\left|\\nabla{H}\\right|^{n-1}*\\nabla{H})}"
+    expected = "\\frac{\\partial H}{\\partial t}=\\nabla \\cdot {(\\Gamma*H^{n+2}*\\left|\\nabla{H}\\right|^{n-1}*\\nabla{H})}"
     # check for route's existence
     assert (
         any(route.path == endpoint for route in app.routes) == True
@@ -50,7 +50,7 @@ async def test_post_image_to_latex_base64():
     # see https://fastapi.tiangolo.com/advanced/async-tests/#async-tests
     async with AsyncClient(app=app, base_url="http://eqn-to-latex-base64-test") as ac:
         response = await ac.post(endpoint, data=img_b64)
-    expected = "\\frac{d H}{dt}=\\nabla \\cdot {(\\Gamma*H^{n+2}*\\left|\\nabla{H}\\right|^{n-1}*\\nabla{H})}"
+    expected = "\\frac{\\partial H}{\\partial t}=\\nabla \\cdot {(\\Gamma*H^{n+2}*\\left|\\nabla{H}\\right|^{n-1}*\\nabla{H})}"
     # check for route's existence
     assert (
         any(route.path == endpoint for route in app.routes) == True

diff --git a/skema/rest/tests/test_isa.py b/skema/rest/tests/test_isa.py
@@ -37,7 +37,7 @@ def test_align_eqns():
     ), f"Response should be 1.0, but instead received {response.text}"
     # check response of union_graph
     assert (
-        json.loads(response.text)["union_graph"] == expected
+        str(json.loads(response.text)["union_graph"]) == expected
     ), f"Response should be {expected}, but instead received {response.text}"
 
 

diff --git a/skema/skema-rs/mathml/src/acset.rs b/skema/skema-rs/mathml/src/acset.rs
@@ -991,4 +991,4 @@ impl From<Vec<FirstOrderODE>> for RegNet {
             metadata: None,
         }
     }
-}
+}
diff --git a/skema/skema-rs/mathml/src/ast.rs b/skema/skema-rs/mathml/src/ast.rs
@@ -1,23 +1,29 @@
 use derive_new::new;
+use schemars::JsonSchema;
 use std::fmt;
 use utoipa::ToSchema;
-use schemars::JsonSchema;
 pub mod operator;
 use operator::Operator;
 use serde::{Deserialize, Serialize};
 //use crate::ast::MathExpression::SummationOp;
 
 /// Represents identifiers such as variables, function names, constants.
 /// E.g. x , sin, n
-#[derive(Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema)]
+#[derive(
+    Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema,
+)]
 pub struct Mi(pub String);
 
 /// Represents groups of any subexpressions
 /// E.g. For a given expression: 2x+4 -->  2 and x are grouped together
-#[derive(Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema)]
+#[derive(
+    Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema,
+)]
 pub struct Mrow(pub Vec<MathExpression>);
 
-#[derive(Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema)]
+#[derive(
+    Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema,
+)]
 pub enum Type {
     Integer,
     Rational,
@@ -35,7 +41,9 @@ pub enum Type {
 
 /// Represents content identifiers such that variables can be have type attribute
 /// to specify what it represents. E.g. function, vector, real,...
-#[derive(Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema)]
+#[derive(
+    Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema,
+)]
 pub struct Ci {
     pub r#type: Option<Type>,
     pub content: Box<MathExpression>,
@@ -44,22 +52,28 @@ pub struct Ci {
 
 /// Represents the differentiation operator `diff` for functions or expresions `func`
 /// E.g. df/dx
-#[derive(Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema)]
+#[derive(
+    Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema,
+)]
 pub struct Differential {
     pub diff: Box<MathExpression>,
     pub func: Box<MathExpression>,
 }
 
 /// Represents sum operator with terms that are summed over
 /// E.g. sum_{i=1}^{K} f(x_i)
-#[derive(Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema)]
+#[derive(
+    Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema,
+)]
 pub struct SummationMath {
     pub op: Box<MathExpression>,
     pub func: Box<MathExpression>,
 }
 
 /// Integral operation represents integral over math expressions
-#[derive(Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema)]
+#[derive(
+    Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema,
+)]
 pub struct Integral {
     pub op: Box<MathExpression>,
     pub integrand: Box<MathExpression>,
@@ -68,24 +82,61 @@ pub struct Integral {
 
 /// Represents Hat operator and the contents the hat operator is being applied to.
 /// E.g. f \hat{x}, where `op` will be \hat{x}, `comp` with be the contents
-#[derive(Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema)]
+#[derive(
+    Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema,
+)]
 pub struct HatComp {
     pub op: Box<MathExpression>,
     pub comp: Box<MathExpression>,
 }
 
 /// Laplacian operator of vector calculus which takes in argument `comp`.
 /// E.g. ∇^2 f
-#[derive(Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema)]
+#[derive(
+    Debug, Ord, PartialOrd, PartialEq, Eq, Clone, Hash, new, Deserialize, Serialize, JsonSchema,
+)]
 pub struct LaplacianComp {
     pub op: Box<MathExpression>,
     pub comp: Ci,
 }
 
+/// Handles ↓  such that {comp}↓_{sub}^{sup} can parse
+#[derive(
+    Debug,
+    Ord,
+    PartialOrd,
+    PartialEq,
+    Eq,
+    Clone,
+    Hash,
+    new,
+    Deserialize,
+    Serialize,
+    ToSchema,
+    JsonSchema,
+)]
+pub struct DownArrow {
+    pub sub: Option<Box<MathExpression>>,
+    pub sup: Option<Box<MathExpression>>,
+    pub comp: Box<MathExpression>,
+}
+
 /// The MathExpression enum is not faithful to the corresponding element type in MathML 3
 /// (https://www.w3.org/TR/MathML3/appendixa.html#parsing_MathExpression)
 #[derive(
-    Debug, PartialOrd, Ord, PartialEq, Eq, Clone, Hash, Default, new, Deserialize, Serialize, ToSchema, JsonSchema
+    Debug,
+    PartialOrd,
+    Ord,
+    PartialEq,
+    Eq,
+    Clone,
+    Hash,
+    Default,
+    new,
+    Deserialize,
+    Serialize,
+    ToSchema,
+    JsonSchema,
 )]
 pub enum MathExpression {
     Mi(Mi),
@@ -128,9 +179,9 @@ pub enum MathExpression {
     Integral(Integral),
     LaplacianComp(LaplacianComp),
     /// Represents closed surface integral over contents. E.g. \\oiint_S ∇ \cdot T dS
-    SurfaceClosedIntegral(Box<MathExpression>),
-    /// Represents closed surface integral over contents where integration E.g. \\oiint_S ∇ \cdot dS
-    SurfaceClosedIntegralNoIntVar(Box<MathExpression>),
+    SurfaceIntegral(Box<MathExpression>),
+    /// ↓ as an operator e.g. I↓ indicates downward diffuse radiative fluxes per unit indcident flux
+    DownArrow(DownArrow),
     #[default]
     None,
 }
@@ -193,9 +244,15 @@ impl fmt::Display for MathExpression {
                 write!(f, "{op}(")?;
                 write!(f, "{comp})")
             }
-            MathExpression::SurfaceClosedIntegral(row) => {
+            MathExpression::SurfaceIntegral(row) => {
                 write!(f, "{row})")
             }
+            MathExpression::DownArrow(DownArrow { sub, sup, comp }) => match (sub, sup) {
+                (Some(low), Some(up)) => write!(f, "{comp}↓_{{{low}}}^{{{up}}}"),
+                (Some(low), None) => write!(f, "{comp}↓_{{{low}}}"),
+                (None, Some(up)) => write!(f, "{comp}↓^{{{up}}}"),
+                (None, None) => write!(f, "{comp}↓"),
+            },
             expression => write!(f, "{expression:?}"),
         }
     }