1.0.2

.github/workflows/build.yml

@@ -21,7 +21,7 @@ jobs:
       fail-fast: true
       matrix:
         os: [ 'ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.8','3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - name: Check out mdal-python
@@ -80,7 +80,7 @@ jobs:
 
     - name: Publish package - test
       uses: pypa/gh-action-pypi-publish@release/v1
-      if: github.event_name != 'release'
+      if: github.event_name == 'pull_request' && github.event.action == 'closed' && github.event.pull_request.merged == true
       with:
         user: __token__
         password: ${{ secrets.PYPI_TEST_TOKEN }}

.gitignore

@@ -43,3 +43,5 @@ mdal.egg-info/
 mdal-python.code-workspace
 mdal-pypi/LICENSE
 mdal-pypi/README.rst
+test/results_3di.nc
+

CHANGES.rst

@@ -1,13 +1,16 @@
 Changes
 --------------------------------------------------------------------------------
 
-2.0.0
+1.0.2
 -----
 
-UNDER DEVELOPMENT
+- fix memory leaks and inconsistencies around the Datagroup object (#11)
+
+1.0.1
+-----
+
+- Add the PyPI package
 
-- fix memory leaks and inconsistencies around the Datagroup object
-- remove Open3D integration to separate package
 
 1.0.0
 -----

mdal/DatasetGroup.cpp

@@ -122,8 +122,14 @@ PyArrayObject* Data::getDataAsDouble(int index)
         MDAL_SetStatus(MDAL_LogLevel::Error, MDAL_Status::Err_FailToWriteToDisk, "Could not import numpy.core.multiarray.");
         return (PyArrayObject*)defaultArray();
     }
+
+    MDAL_DatasetH datasetH = MDAL_G_dataset(m_data, index);
+    if ( MDAL_LastStatus() != MDAL_Status::None)
+    {
+        return (PyArrayObject*)defaultArray();
+    }
 
-    npy_intp valueCount = (npy_intp)MDAL_D_valueCount( MDAL_G_dataset(m_data, index));
+    npy_intp valueCount = (npy_intp)MDAL_D_valueCount( datasetH);
     int dims;
     MDAL_DataType type;
     if (MDAL_G_hasScalarData(m_data)) 
@@ -190,15 +196,16 @@ PyArrayObject* Data::getDataAsDouble(int index)
     }
 
     Py_XDECREF(dict);
+    Py_XDECREF(titles);
+    Py_XDECREF(formats);
+    Py_XDECREF(m_dataset);
 
     // This is a valueCount array.
-    PyArrayObject* dataset = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, dtype,
+    m_dataset = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, dtype,
             1, &valueCount, 0, nullptr, NPY_ARRAY_CARRAY, nullptr);
 
     double* buffer = new double[dims * 1024];
     size_t count = 0;
-    int bufs = std::ceil(valueCount/1024);
-    if (bufs == 0) bufs = 1;
     int indexStart = 0;
     int next = 1024;
 
@@ -207,7 +214,7 @@ PyArrayObject* Data::getDataAsDouble(int index)
         int remain = valueCount - indexStart;
         if (remain < 1024) next = remain;
         if (remain <= 0 ) break;
-        count = MDAL_D_data(MDAL_G_dataset(m_data, index), indexStart, next , type, buffer);
+        count = MDAL_D_data(datasetH, indexStart, next , type, buffer);
         if (count != next) 
         {
             delete [] buffer;
@@ -216,7 +223,7 @@ PyArrayObject* Data::getDataAsDouble(int index)
         int idx = 0;
         for (int i = 0; i < count; i++) 
         {
-            char* p = (char *)PyArray_GETPTR1(dataset, indexStart + i);
+            char* p = (char *)PyArray_GETPTR1(m_dataset, indexStart + i);
 
             for (int l =0; l < dims; l++)
             {
@@ -230,7 +237,7 @@ PyArrayObject* Data::getDataAsDouble(int index)
     }
     delete [] buffer;
 
-    return dataset;
+    return m_dataset;
 }
 
 PyArrayObject* Data::getDataAsVolumeIndex(int index)
@@ -244,8 +251,13 @@ PyArrayObject* Data::getDataAsVolumeIndex(int index)
         MDAL_SetStatus(MDAL_LogLevel::Error, MDAL_Status::Err_FailToWriteToDisk, "Could not import numpy.core.multiarray.");
         return (PyArrayObject*)defaultArray();
     }
+
+    if ( MDAL_LastStatus() != MDAL_Status::None)
+    {
+        return (PyArrayObject*)defaultArray();
+    }
 
-    npy_intp valueCount = (npy_intp)MDAL_M_faceCount( MDAL_G_mesh(m_data));
+    npy_intp valueCount = (npy_intp)MDAL_M_faceCount( MDAL_G_mesh(m_data) );
 
     PyObject* dict = PyDict_New();
     PyObject* formats = PyList_New(1);
@@ -265,15 +277,16 @@ PyArrayObject* Data::getDataAsVolumeIndex(int index)
     }
 
     Py_XDECREF(dict);
+    Py_XDECREF(titles);
+    Py_XDECREF(formats);
+    Py_XDECREF(m_dataset);
 
     // This is a dsCount x valueCount array.
-    PyArrayObject* dataset = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, dtype,
+    m_dataset = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, dtype,
             1, &valueCount, 0, nullptr, NPY_ARRAY_CARRAY, nullptr);
 
     int* buffer = new int[1024];
     size_t count = 0;
-    int bufs = std::ceil(valueCount/1024);
-    if (bufs == 0) bufs = 1;
     int indexStart = 0;
     int next = 1024;
 
@@ -282,7 +295,7 @@ PyArrayObject* Data::getDataAsVolumeIndex(int index)
         int remain = valueCount - indexStart;
         if (remain < 1024) next = remain;
         if (remain <= 0 ) break;
-        count = MDAL_D_data(MDAL_G_dataset(m_data, index), indexStart, next , MDAL_DataType::FACE_INDEX_TO_VOLUME_INDEX_INTEGER, buffer);
+        count = MDAL_D_data( MDAL_G_dataset(m_data, index), indexStart, next , MDAL_DataType::FACE_INDEX_TO_VOLUME_INDEX_INTEGER, buffer);
         if (count != next) 
         {
             delete [] buffer;
@@ -291,7 +304,7 @@ PyArrayObject* Data::getDataAsVolumeIndex(int index)
         int idx = 0;
         for (int i = 0; i < count; i++) 
         {
-            char* p = (char *)PyArray_GETPTR1(dataset, indexStart + i);
+            char* p = (char *)PyArray_GETPTR1(m_dataset, indexStart + i);
             uint32_t val = (uint32_t)buffer[idx];
             idx++;
             std::memcpy(p, &val, 4);
@@ -300,12 +313,12 @@ PyArrayObject* Data::getDataAsVolumeIndex(int index)
     }
     delete [] buffer;
 
-    return dataset;
+    return m_dataset;
 }
 
 PyArrayObject* Data::getDataAsLevelCount(int index)
 {
-        if (! m_data) 
+    if (! m_data) 
         return (PyArrayObject*)defaultArray();
 
     MDAL_ResetStatus();
@@ -314,6 +327,12 @@ PyArrayObject* Data::getDataAsLevelCount(int index)
         MDAL_SetStatus(MDAL_LogLevel::Error, MDAL_Status::Err_FailToWriteToDisk, "Could not import numpy.core.multiarray.");
         return (PyArrayObject*)defaultArray();
     }
+
+    MDAL_DatasetH datasetH = MDAL_G_dataset(m_data, index);
+    if ( MDAL_LastStatus() != MDAL_Status::None)
+    {
+        return (PyArrayObject*)defaultArray();
+    }
 
     npy_intp valueCount = (npy_intp)MDAL_M_faceCount( MDAL_G_mesh(m_data));
 
@@ -335,15 +354,16 @@ PyArrayObject* Data::getDataAsLevelCount(int index)
     }
 
     Py_XDECREF(dict);
+    Py_XDECREF(titles);
+    Py_XDECREF(formats);
+    Py_XDECREF(m_dataset);
 
     // This is a dsCount x valueCount array.
-    PyArrayObject* dataset = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, dtype,
+    m_dataset = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, dtype,
             1, &valueCount, 0, nullptr, NPY_ARRAY_CARRAY, nullptr);
 
     int* buffer = new int[1024];
     size_t count = 0;
-    int bufs = std::ceil(valueCount/1024);
-    if (bufs == 0) bufs = 1;
     int indexStart = 0;
     int next = 1024;
 
@@ -352,7 +372,7 @@ PyArrayObject* Data::getDataAsLevelCount(int index)
         int remain = valueCount - indexStart;
         if (remain < 1024) next = remain;
         if (remain <= 0 ) break;
-        count = MDAL_D_data(MDAL_G_dataset(m_data, index), indexStart, next , MDAL_DataType::VERTICAL_LEVEL_COUNT_INTEGER, buffer);
+        count = MDAL_D_data( datasetH, indexStart, next , MDAL_DataType::VERTICAL_LEVEL_COUNT_INTEGER, buffer);
 
         if (count != next) 
         {
@@ -362,7 +382,7 @@ PyArrayObject* Data::getDataAsLevelCount(int index)
         int idx = 0;
         for (int i = 0; i < count; i++) 
         {
-            char* p = (char *)PyArray_GETPTR1(dataset, indexStart + i);
+            char* p = (char *)PyArray_GETPTR1(m_dataset, indexStart + i);
             uint32_t val = (uint32_t)buffer[idx];
             idx++;
             std::memcpy(p, &val, 4);
@@ -371,7 +391,7 @@ PyArrayObject* Data::getDataAsLevelCount(int index)
     }
     delete [] buffer;
 
-    return dataset;
+    return m_dataset;
 }
 
 PyArrayObject* Data::getDataAsLevelValue(int index)
@@ -385,6 +405,12 @@ PyArrayObject* Data::getDataAsLevelValue(int index)
         MDAL_SetStatus(MDAL_LogLevel::Error, MDAL_Status::Err_FailToWriteToDisk, "Could not import numpy.core.multiarray.");
         return (PyArrayObject*)defaultArray();
     }
+
+    MDAL_DatasetH datasetH = MDAL_G_dataset(m_data, index);
+    if ( MDAL_LastStatus() != MDAL_Status::None)
+    {
+        return (PyArrayObject*)defaultArray();
+    }
 
     npy_intp valueCount = (npy_intp)MDAL_M_faceCount( MDAL_G_mesh(m_data)) + (npy_intp)MDAL_D_valueCount( MDAL_G_dataset(m_data, index));
 
@@ -406,15 +432,16 @@ PyArrayObject* Data::getDataAsLevelValue(int index)
     }
 
     Py_XDECREF(dict);
+    Py_XDECREF(titles);
+    Py_XDECREF(formats);
+    Py_XDECREF(m_dataset);
 
     // This is a dsCount x valueCount array.
-    PyArrayObject* dataset = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, dtype,
+    m_dataset = (PyArrayObject *)PyArray_NewFromDescr(&PyArray_Type, dtype,
             1, &valueCount, 0, nullptr, NPY_ARRAY_CARRAY, nullptr);
 
     double* buffer = new double[1024];
     size_t count = 0;
-    int bufs = std::ceil(valueCount/1024);
-    if (bufs == 0) bufs = 1;
     int indexStart = 0;
     int next = 1024;
 
@@ -423,7 +450,7 @@ PyArrayObject* Data::getDataAsLevelValue(int index)
         int remain = valueCount - indexStart;
         if (remain < 1024) next = remain;
         if (remain <= 0 ) break;
-        count = MDAL_D_data(MDAL_G_dataset(m_data, index), indexStart, next , MDAL_DataType::VERTICAL_LEVEL_DOUBLE, buffer);
+        count = MDAL_D_data( datasetH, indexStart, next , MDAL_DataType::VERTICAL_LEVEL_DOUBLE, buffer);
 
         if (count != next) 
         {
@@ -433,15 +460,15 @@ PyArrayObject* Data::getDataAsLevelValue(int index)
         int idx = 0;
         for (int i = 0; i < count; i++) 
         {
-            char* p = (char *)PyArray_GETPTR1(dataset, indexStart + i);
+            char* p = (char *)PyArray_GETPTR1(m_dataset, indexStart + i);
             double val = buffer[idx];
             idx++;
             std::memcpy(p, &val, 8);
         }
         indexStart += count;
     }
     delete [] buffer;
-    return dataset;
+    return m_dataset;
 }
 
 MDAL_Status Data::setDataAsDouble(PyArrayObject* data, double time)

mdal/PyMesh.cpp

@@ -225,7 +225,9 @@ PyArrayObject *Mesh::getFaces()
         if (PyArray_DescrConverter(dict, &dtype) == NPY_FAIL)
             {}
     //         throw pdal_error("Unable to build numpy dtype");
-        Py_XDECREF(dict);
+    Py_XDECREF(dict);
+    Py_XDECREF(titles);
+    Py_XDECREF(formats);
 
         npy_intp size = (npy_intp)faceCount();
 
@@ -292,7 +294,9 @@ PyArrayObject *Mesh::getEdges()
         if (PyArray_DescrConverter(dict, &dtype) == NPY_FAIL)
             {}
     //         throw pdal_error("Unable to build numpy dtype");
-        Py_XDECREF(dict);
+    Py_XDECREF(dict);
+    Py_XDECREF(titles);
+    Py_XDECREF(formats);
 
         npy_intp size = (npy_intp)edgeCount();
 
@@ -450,8 +454,9 @@ bool Mesh::addFaces(PyArrayObject* faces, long int count){
     PyObject *names_dict = dtype->fields;
     PyObject *names = PyDict_Keys(names_dict);
     PyObject *values = PyDict_Values(names_dict);
-    if (!names || !values) {}
+    if (!names || !values) {
         //throw pdal_error("Bad field specification in numpy array.");
+    }
 
     if (numFields< 3) {}
         //throw pdal_error("Faces"

mdal/__init__.py

@@ -11,7 +11,7 @@
 
 from mdal.transform import MDAL_transform
 
-__version__ = '1.0.1'
+__version__ = '1.0.2'
 
 
 class Info(object):

mdal/libmdalpython.pyx

@@ -228,20 +228,21 @@ cdef class Datasource:
 
     def __cinit__(self, uri: Path, driver_name : str = None):   
         self.uri = str(uri)
-        if type(uri) != Path:
-            path = Path(uri)
+        if type(uri) == str:
+            uri = Path(uri)
+        print(uri)
         if driver_name:
             self.driver_name = driver_name
             return
-        if path.is_file():
+        if uri.is_file():
             try:
                 meshes = self.meshes
                 if len(meshes) > 0:
                     self.driver_name = meshes[0].split(":")[0]
                     return
             except Exception:
                 pass
-        ex = path.suffix
+        ex = uri.suffix
         for driver in drivers():
             if ex in driver.filters:
                 self.driver_name = driver.name