diff image_math.py @ 0:33b2ca53a566 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/image_math.py	Sat Mar 09 22:04:19 2024 +0000
@@ -0,0 +1,90 @@
+import argparse
+import ast
+import operator
+
+import numpy as np
+import skimage.io
+
+
+supported_operators = {
+    ast.Add: operator.add,
+    ast.Sub: operator.sub,
+    ast.Mult: operator.mul,
+    ast.Div: operator.truediv,
+    ast.FloorDiv: operator.floordiv,
+    ast.Pow: operator.pow,
+    ast.USub: operator.neg,
+}
+
+
+supported_functions = {
+    'sqrt': np.sqrt,
+    'abs': abs,
+}
+
+
+def eval_ast_node(node, inputs):
+    """
+    Evaluates a node of the syntax tree.
+    """
+
+    # Numeric constants evaluate to numeric values.
+    if isinstance(node, ast.Constant):
+        assert type(node.value) in (int, float)
+        return node.value
+
+    # Variables are looked up from the inputs and resolved.
+    if isinstance(node, ast.Name):
+        assert node.id in inputs.keys()
+        return inputs[node.id]
+
+    # Binary operators are evaluated based on the `supported_operators` dictionary.
+    if isinstance(node, ast.BinOp):
+        assert type(node.op) in supported_operators.keys(), node.op
+        op = supported_operators[type(node.op)]
+        return op(eval_ast_node(node.left, inputs), eval_ast_node(node.right, inputs))
+
+    # Unary operators are evaluated based on the `supported_operators` dictionary.
+    if isinstance(node, ast.UnaryOp):
+        assert type(node.op) in supported_operators.keys(), node.op
+        op = supported_operators[type(node.op)]
+        return op(eval_ast_node(node.operand, inputs))
+
+    # Function calls are evaluated based on the `supported_functions` dictionary.
+    if isinstance(node, ast.Call):
+        assert len(node.args) == 1 and len(node.keywords) == 0
+        assert node.func.id in supported_functions.keys(), node.func.id
+        func = supported_functions[node.func.id]
+        return func(eval_ast_node(node.args[0], inputs))
+
+    # The node is unsupported and could not be evaluated.
+    raise TypeError(f'Unsupported node type: "{node}"')
+
+
+def eval_expression(expr, inputs):
+    return eval_ast_node(ast.parse(expr, mode='eval').body, inputs)
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--expression', type=str, required=True)
+    parser.add_argument('--output', type=str, required=True)
+    parser.add_argument('--input', default=list(), action='append', required=True)
+    args = parser.parse_args()
+
+    inputs = dict()
+    im_shape = None
+    for input in args.input:
+        name, filepath = input.split(':')
+        im = skimage.io.imread(filepath)
+        assert name not in inputs, 'Input name "{name}" is ambiguous.'
+        inputs[name] = im
+        if im_shape is None:
+            im_shape = im.shape
+        else:
+            assert im.shape == im_shape, 'Input images differ in size and/or number of channels.'
+
+    result = eval_expression(args.expression, inputs)
+
+    skimage.io.imsave(args.output, result)