Add xml layout parameter to open

Author: achaikou

python/segyio/open.py

@@ -43,7 +43,9 @@ def open(filename, mode="r", iline = None,
                              strict = True,
                              ignore_geometry = False,
                              endian = None,
-                             encoding = None):
+                             encoding = None,
+                             layout_xml = None
+                             ):
     """Open a segy file.
 
     Opens a segy file and tries to figure out its sorting, inline numbers,
@@ -110,6 +112,10 @@ def open(filename, mode="r", iline = None,
         into latin-1 encoding as per SEG-Y specification. For ascii encoding
         data would be returned as is.
 
+    layout_xml: bytearray
+        SEG-Y revision 2.1 D8 xml layout. Takes precedence over layout
+        definition xml inside the file.
+
     Returns
     -------
 
@@ -130,6 +136,9 @@ def open(filename, mode="r", iline = None,
     .. versionchanged:: 1.8
         endian argument
 
+    .. versionchanged:: 2.0
+       Support for SEG-Y revision 2.1
+
     When a file is opened non-strict, only raw traces access is allowed, and
     using modes such as ``iline`` raise an error.
 
@@ -168,7 +177,7 @@ def open(filename, mode="r", iline = None,
 
     return _open(
         FileDatasourceDescriptor(filename, mode),
-        iline, xline, strict, ignore_geometry, endian, encoding
+        iline, xline, strict, ignore_geometry, endian, encoding, layout_xml
     )
 
 
@@ -179,7 +188,8 @@ def open_with(stream,
               ignore_geometry=False,
               endian=None,
               encoding=None,
-              minimize_requests_number=True
+              minimize_requests_number=True,
+              layout_xml = None
               ):
     """
     Opens a segy file from a stream.
@@ -209,7 +219,7 @@ def open_with(stream,
             stream,
             minimize_requests_number
         ),
-        iline, xline, strict, ignore_geometry, endian, encoding
+        iline, xline, strict, ignore_geometry, endian, encoding, layout_xml
     )
 
 
@@ -220,6 +230,7 @@ def open_from_memory(memory_buffer,
                    ignore_geometry=False,
                    endian=None,
                    encoding=None,
+                   layout_xml = None
                    ):
     """
     Opens a segy file from memory.
@@ -241,7 +252,7 @@ def open_from_memory(memory_buffer,
         MemoryBufferDatasourceDescriptor(
             memory_buffer
         ),
-        iline, xline, strict, ignore_geometry, endian, encoding
+        iline, xline, strict, ignore_geometry, endian, encoding, layout_xml
     )
 
 
@@ -252,6 +263,7 @@ def _open(datasource_descriptor,
           ignore_geometry=False,
           endian=None,
           encoding=None,
+          layout_xml = None
           ):
 
     fd = datasource_descriptor.make_segyfile_descriptor()
@@ -265,7 +277,8 @@ def _open(datasource_descriptor,
         endianness=to_c_endianness(endian),
         encoding=to_c_encoding(encoding),
         iline=iline,
-        xline=xline
+        xline=xline,
+        layout_xml=layout_xml
     )
     metrics = fd.metrics()
 

python/segyio/segyio.cpp

@@ -650,21 +650,25 @@ PyObject* segyopen( segyfd* self, PyObject* args, PyObject* kwargs ) {
     int encoding = -1;
     PyObject *py_iline = Py_None;
     PyObject *py_xline = Py_None;
+    PyObject* py_layout_xml = Py_None;
+
     static const char* keywords[] = {
         "endianness",
         "encoding",
         "iline",
         "xline",
+        "layout_xml",
         NULL
     };
 
     if( !PyArg_ParseTupleAndKeywords(
-            args, kwargs, "|iiOO",
+            args, kwargs, "|iiOOO",
             const_cast<char**>( keywords ),
             &endianness,
             &encoding,
             &py_iline,
-            &py_xline
+            &py_xline,
+            &py_layout_xml
         ) ) {
         return NULL;
     }
@@ -680,8 +684,18 @@ PyObject* segyopen( segyfd* self, PyObject* args, PyObject* kwargs ) {
     if( err ) return Error( err );
 
     std::vector<char> layout_stanza_data;
-    err = extract_layout_stanza( self, layout_stanza_data );
-    if( err ) return Error( err );
+    if( py_layout_xml != Py_None ) {
+        buffer_guard layout_xml( py_layout_xml, PyBUF_CONTIG );
+        layout_stanza_data.resize( layout_xml.len() );
+        std::memcpy(
+            layout_stanza_data.data(),
+            layout_xml.buf<char>(),
+            layout_xml.len()
+        );
+    } else {
+        err = extract_layout_stanza( self, layout_stanza_data );
+        if( err ) return Error( err );
+    }
 
     err = set_traceheader_mappings( self, layout_stanza_data, py_iline, py_xline );
     if( err ) return NULL;

python/test/segy.py

@@ -2639,4 +2639,43 @@ def test_revision_2_1_file_creation(tmpdir):
             dst.trace = src.trace
             dst.traceheader = src.traceheader
 
+        with segyio.open(fresh, "r+", ignore_geometry=True) as dst:
+            pass
+
     assert filecmp.cmp(orig, fresh)
+
+
+def test_custom_layout_xml(tmpdir):
+    small = str(testdata / 'small.sgy')
+    orig = str(testdata / 'trace-header-extensions.sgy')
+    fresh = tmpdir / '2.1-headers-not-copied.sgy'
+    with segyio.open(orig) as src:
+        spec = segyio.spec()
+        spec.format = int(src.format)
+        spec.sorting = int(src.sorting)
+        spec.samples = src.samples
+        spec.ilines = src.ilines
+        spec.xlines = src.xlines
+        spec.ext_headers = 0
+        spec.traceheader_count = src.traceheader_count
+        spec.tracecount = src.tracecount
+
+        layout = src.stanza[0]
+
+        with segyio.open(small, "r") as f:
+            assert len(f.tracefield[0].names()) == 92
+        with segyio.open(small, "r", layout_xml=layout) as f:
+            assert len(f.tracefield[0].names()) == 8
+
+        with segyio.create(fresh, spec, layout_xml=layout) as dst:
+            dst.bin = src.bin
+            dst.bin[BinField.ExtendedHeaders] = 0
+            dst.trace = src.trace
+            dst.traceheader = src.traceheader
+
+        with pytest.raises(KeyError, match="traceheader mapping for 'PRIVATE1' not found"):
+            segyio.open(fresh, "r", ignore_geometry=True)
+
+        with segyio.open(fresh, "r", ignore_geometry=True, layout_xml=layout) as f:
+            assert f.tracefield.names() == ['SEG00000', 'SEG00001', 'PRIVATE1']
+            assert f.tracefield.SEG00001.names() == ['linetrc', 'header_name']