medpython 1.2.0__tar.gz → 1.2.1__tar.gz

{medpython-1.2.0 → medpython-1.2.1}/CMakeLists.txt

@@ -128,6 +128,20 @@ else ()
 endif()
 # XGboost
 
+set(XGBOOST_VERSION "3.4.1")
+
+if(XGBOOST_VERSION VERSION_GREATER "2.0.3")
+    set(XGBOOST_TARGET_DIR "")
+else()
+    set(XGBOOST_TARGET_DIR "cpp_src")
+endif()
+
+if(XGBOOST_VERSION VERSION_GREATER_EQUAL "3.0.0")
+    set(XGBOOST_DOWNLOAD "-src")
+else()
+    set(XGBOOST_DOWNLOAD "")
+endif()
+
 set(XGBOOST_STATIC_FALLBACK OFF)
 find_package(xgboost QUIET)
 
@@ -154,9 +168,9 @@ else()
     set(XGBOOST_STATIC_FALLBACK ON)
     FetchContent_Declare(
         xgboost
-        URL      https://github.com/dmlc/xgboost/releases/download/v2.0.3/xgboost-2.0.3.tar.gz
+        URL      https://github.com/dmlc/xgboost/releases/download/v${XGBOOST_VERSION}/xgboost${XGBOOST_DOWNLOAD}-${XGBOOST_VERSION}.tar.gz
         DOWNLOAD_EXTRACT_TIMESTAMP ON
-        SOURCE_SUBDIR cpp_src
+        SOURCE_SUBDIR ${XGBOOST_TARGET_DIR}
     )
 
     set(BUILD_STATIC_LIB ON CACHE BOOL "Build XGBoost as a static library" FORCE)
@@ -168,9 +182,8 @@ else()
     endif()
     FetchContent_MakeAvailable(xgboost)
 
-    include_directories(SYSTEM ${xgboost_SOURCE_DIR}/cpp_src/include)          
-    include_directories(SYSTEM ${xgboost_SOURCE_DIR}/cpp_src/rabit/include)
-    include_directories(SYSTEM ${xgboost_SOURCE_DIR}/cpp_src/dmlc-core/include)
+    include_directories(SYSTEM ${xgboost_SOURCE_DIR}/${XGBOOST_TARGET_DIR}/include)
+    include_directories(SYSTEM ${xgboost_SOURCE_DIR}/${XGBOOST_TARGET_DIR}/dmlc-core/include)
 
     set(XGBOOST_TARGET xgboost)
 endif()

{medpython-1.2.0/src/medpython.egg-info → medpython-1.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: medpython
-Version: 1.2.0
+Version: 1.2.1
 Summary: Medial EarlySign Python
 Author: Alon Lanyado
 License-Expression: MIT

{medpython-1.2.0 → medpython-1.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "medpython"
-version = "1.2.0"
+version = "1.2.1"
 description = "Medial EarlySign Python"
 readme = "README.md"
 license = "MIT"

{medpython-1.2.0 → medpython-1.2.1}/src/med/cpp_code/Internal/AlgoMarker/CMakeLists.txt

@@ -104,11 +104,25 @@ else ()
 endif()
 
 # XGboost
+set(XGBOOST_VERSION "3.0.5")
+
+if(XGBOOST_VERSION VERSION_GREATER "2.0.3")
+    set(XGBOOST_TARGET_DIR "")
+else()
+    set(XGBOOST_TARGET_DIR "cpp_src")
+endif()
+
+if(XGBOOST_VERSION VERSION_GREATER_EQUAL "3.0.0")
+    set(XGBOOST_DOWNLOAD "-src")
+else()
+    set(XGBOOST_DOWNLOAD "")
+endif()
+
 FetchContent_Declare(
     xgboost
-    URL      https://github.com/dmlc/xgboost/releases/download/v2.0.3/xgboost-2.0.3.tar.gz
+    URL      https://github.com/dmlc/xgboost/releases/download/v${XGBOOST_VERSION}/xgboost${XGBOOST_DOWNLOAD}-${XGBOOST_VERSION}.tar.gz
     DOWNLOAD_EXTRACT_TIMESTAMP ON
-    SOURCE_SUBDIR cpp_src
+    SOURCE_SUBDIR ${XGBOOST_TARGET_DIR}
 )
 
 set(BUILD_STATIC_LIB ON CACHE BOOL "Build XGBoost as a static library" FORCE)
@@ -117,9 +131,10 @@ set(XGBOOST_BUILD_TESTS OFF CACHE BOOL "" FORCE)
 
 FetchContent_MakeAvailable(xgboost)
 
-include_directories(SYSTEM ${xgboost_SOURCE_DIR}/cpp_src/include)          
-include_directories(SYSTEM ${xgboost_SOURCE_DIR}/cpp_src/rabit/include)
-include_directories(SYSTEM ${xgboost_SOURCE_DIR}/cpp_src/dmlc-core/include)
+
+
+include_directories(SYSTEM ${xgboost_SOURCE_DIR}/${XGBOOST_TARGET_DIR}/include)          
+include_directories(SYSTEM ${xgboost_SOURCE_DIR}/${XGBOOST_TARGET_DIR}/dmlc-core/include)
 
 # LightGBM
 FetchContent_Declare(

{medpython-1.2.0 → medpython-1.2.1}/src/med/cpp_code/Internal/InfraMed/InfraMed/InMemData.cpp

@@ -1,182 +1,182 @@
-#include "InfraMed.h"
-
-#undef LOCAL_SECTION
-#define LOCAL_SECTION LOG_REP
-#define LOCAL_LEVEL	LOG_DEF_LEVEL
-extern MedLogger global_logger;
-
-int InMemRepData::insertData_to_buffer(int pid, int sid, int *time_data, float *val_data, int n_time, int n_val, 
-	const MedSignals &sigs, map<pair<int, int>, pair<int, vector<char>>> &data) {
-	int n_time_ch = sigs.Sid2Info[sid].n_time_channels;
-	int n_val_ch = sigs.Sid2Info[sid].n_val_channels;
-
-	int n_elem_by_time = 0;
-	int n_elem_by_val = 0;
-	if (n_time_ch > 0) n_elem_by_time = n_time/n_time_ch;
-	if (n_val_ch > 0) n_elem_by_val = n_val/n_val_ch;
-
-
-	//MLOG(">>>> sid %d ch(%d,%d) elem(%d,%d) n(%d,%d)\n", sid, n_time_ch, n_val_ch, n_elem_by_time, n_elem_by_val, n_time, n_val);
-	// a few sanity tests
-	if ((n_time != n_elem_by_time*n_time_ch) || (n_val != n_elem_by_val*n_val_ch) || 
-	    (n_time_ch == 0 && n_time > 0) || (n_val_ch == 0 && n_val > 0) ||
-	    (n_time_ch > 0 && n_time == 0) || (n_val_ch > 0 && n_val == 0) || 
-		(n_time_ch > 0 && n_val_ch > 0 && n_elem_by_time != n_elem_by_val))
-	{
-		MERR("ERROR: InMemRepData: non matching time/value numbers for pid %d, sid %d : needed (%d,%d) per element , got (%d,%d) ...\n",
-			pid, sid, n_time_ch, n_val_ch, n_time, n_val);
-		return -1;
-	}
-	int n_elem = max(n_elem_by_time, n_elem_by_val);
-
-	int len_bytes = sigs.Sid2Info[sid].bytes_len;
-
-	vector<char> elem(len_bytes*n_elem);
-
-	int type = sigs.Sid2Info[sid].type;
-
-	//MLOG("pid %d sid %d type %d len_bytes %d nelem %d\n", pid, sid, type, len_bytes, n_elem);
-	int *tdata = time_data;
-	float *vdata = val_data;
-
-	if (n_time_ch == 0) tdata = NULL;
-	if (n_val_ch == 0) vdata = NULL;
-
-	//MLOG("pid %d sid %d type %d len_bytes %d nelem %d\n", pid, sid, type, len_bytes, n_elem);
-	if (type == T_Generic) {
-		GenericSigVec gsv;
-		gsv.init(sigs.Sid2Info[sid]);
-		gsv.set_data(&elem[0], n_elem);
-		for (int i = 0; i < n_elem; i++) {
-			gsv.Set(i, tdata, vdata);
-			if (tdata) tdata += n_time_ch;
-			if (vdata) vdata += n_val_ch;
-		}
-	}
-	else {
-		for (int i = 0; i < n_elem; i++) {
-			if (MedSignalsSingleElemFill(type, &elem[len_bytes*i], tdata, vdata) < 0) {
-				MERR("ERROR: InMemRepData::insertData failed fill element %d/%d.", i, n_elem);
-				return -1;
-			}
-
-			if (tdata) tdata += n_time_ch;
-			if (vdata) vdata += n_val_ch;
-		}
-	}
-	// all is ready -> we push it to the map
-	pair<int, int> pid_sid(pid, sid);
-	pair<int, vector<char>> n_data;
-	if (data.find(pid_sid) == data.end()) {
-		data[pid_sid] = n_data;
-		data[pid_sid].second = elem;
-		data[pid_sid].first = n_elem;
-		//MLOG("inserted pid %d sid %d nelem %d bytes %d size %d\n", pid, sid, n_elem, len_bytes, elem.size());
-	}
-	else {
-		data[pid_sid].second.insert(data[pid_sid].second.end(), elem.begin(), elem.end());
-		data[pid_sid].first += n_elem;
-	}
-
-	return 0;
-}
-
-//-------------------------------------------------------------------------------------------------------------------
-int InMemRepData::insertData(int pid, const char *sig, int *time_data, float *val_data, int n_time, int n_val)
-{
-	int sid = my_rep->sigs.sid(string(sig));
-	if (sid < 0) {
-		MERR("ERROR: InMemRepData: sig %s in not is signals file (did you read the file\?\?)\n", sig);
-		return -1;
-	}
-	return insertData(pid, sid, time_data, val_data, n_time, n_val);
-
-}
-
-//-------------------------------------------------------------------------------------------------------------------
-int InMemRepData::insertData(int pid, int sid, int *time_data, float *val_data, int n_time, int n_val)
-{
-	return InMemRepData::insertData_to_buffer(pid, sid, time_data, val_data, n_time, n_val, my_rep->sigs, data);
-}
-
-//-------------------------------------------------------------------------------------------------------------------
-int InMemRepData::sort_pid_sid(int pid, int sid)
-{
-	pair<int, int> pid_sid(pid, sid);
-
-	if (data.find(pid_sid) == data.end()) return 0; // nothing to do.
-
-	if (data[pid_sid].first <= 1) return 0; // no need to sort a single variable
-
-	int (*compare_func)(const void *, const void *);
-	GenericSigVec gsv;
-	switch (my_rep->sigs.Sid2Info[sid].type) {
-	case T_Value:				compare_func = &MedSignalsCompareSig<SVal>;				break;
-	case T_DateVal:				compare_func = &MedSignalsCompareSig<SDateVal>;			break;
-	case T_TimeVal:				compare_func = &MedSignalsCompareSig<STimeVal>;			break;
-	case T_DateRangeVal:		compare_func = &MedSignalsCompareSig<SDateRangeVal>;	break;
-	case T_TimeStamp:			compare_func = &MedSignalsCompareSig<STimeStamp>;		break;
-	case T_TimeRangeVal:		compare_func = &MedSignalsCompareSig<STimeRangeVal>;	break;
-	case T_DateVal2:			compare_func = &MedSignalsCompareSig<SDateVal2>;		break;
-	case T_TimeLongVal:			compare_func = &MedSignalsCompareSig<STimeLongVal>;		break;
-	case T_DateShort2:			compare_func = &MedSignalsCompareSig<SDateShort2>;		break;
-	case T_ValShort2:			compare_func = &MedSignalsCompareSig<SValShort2>;		break;
-	case T_ValShort4:			compare_func = &MedSignalsCompareSig<SValShort4>;		break;
-	case T_DateRangeVal2:		compare_func = &MedSignalsCompareSig<SDateRangeVal2>;	break;
-	case T_DateFloat2:			compare_func = &MedSignalsCompareSig<SDateFloat2>;		break;
-	case T_TimeShort4:			compare_func = &MedSignalsCompareSig<STimeShort4>;		break;
-	case T_Generic:
-		gsv.init(my_rep->sigs.Sid2Info[sid]);
-		gsv.inplace_sort_data(&data[pid_sid].second[0], data[pid_sid].first);
-		return 0;
-	//case T_CompactDateVal:		break; // not fully supported yet
-	default: MERR("ERROR:sort_pid_sid Unknown sig_type %d\n", my_rep->sigs.Sid2Info[sid].type);
-		return -1;
-	}
-
-	//MLOG("pid %d sid %d len %d bytes %d first_val %f\n", pid, sid, data[pid_sid].first, my_rep->sigs.Sid2Info[sid].bytes_len, data[pid_sid].second[0]);
-	qsort(&data[pid_sid].second[0], data[pid_sid].first, my_rep->sigs.Sid2Info[sid].bytes_len, compare_func);
-
-	return 0;
-}
-
-//-------------------------------------------------------------------------------------------------------------------
-int InMemRepData::sortData()
-{
-	for (auto &data_elem : data) {
-		//MLOG("Now sorting pid %d sid %d (%s)\n", data_elem.first.first, data_elem.first.second, my_rep->sigs.Sid2Name[data_elem.first.second].c_str());
-		if (sort_pid_sid(data_elem.first.first, data_elem.first.second) < 0) {
-			MERR("FAILED:: InMemRepData::sortData() failed sorting pid %d sid %d\n", data_elem.first.first, data_elem.first.second);
-			return -1;
-		}
-	}
-	return 0;
-}
-
-//-------------------------------------------------------------------------------------------------------------------
-void *InMemRepData::get_from_buffer(int pid, int sid, int &len, const map<pair<int, int>, pair<int, vector<char>>> &data) {
-	pair<int, int> pid_sid(pid, sid);
-	if (data.find(pid_sid) == data.end()) {
-		len = 0;
-		return NULL;
-	}
-
-	len = data.at(pid_sid).first;
-	return (void *)&data.at(pid_sid).second[0];
-}
-
-void * InMemRepData::get(int pid, int sid, int &len)
-{
-	return InMemRepData::get_from_buffer(pid, sid, len, data);
-}
-
-void InMemRepData::erase_pid_data(int pid) {
-	//Erase from data all (pid, sid):
-	for ( auto &it : my_rep->sigs.Name2Sid) {
-		pair<int, int> pid_sid(pid, it.second);
-		if (data.find(pid_sid) != data.end()) {
-			data.erase(pid_sid);
-		}
-	}
-
+#include "InfraMed.h"
+
+#undef LOCAL_SECTION
+#define LOCAL_SECTION LOG_REP
+#define LOCAL_LEVEL	LOG_DEF_LEVEL
+extern MedLogger global_logger;
+
+int InMemRepData::insertData_to_buffer(int pid, int sid, int *time_data, float *val_data, int n_time, int n_val, 
+	const MedSignals &sigs, map<pair<int, int>, pair<int, vector<char>>> &data) {
+	int n_time_ch = sigs.Sid2Info[sid].n_time_channels;
+	int n_val_ch = sigs.Sid2Info[sid].n_val_channels;
+
+	int n_elem_by_time = 0;
+	int n_elem_by_val = 0;
+	if (n_time_ch > 0) n_elem_by_time = n_time/n_time_ch;
+	if (n_val_ch > 0) n_elem_by_val = n_val/n_val_ch;
+
+
+	//MLOG(">>>> sid %d ch(%d,%d) elem(%d,%d) n(%d,%d)\n", sid, n_time_ch, n_val_ch, n_elem_by_time, n_elem_by_val, n_time, n_val);
+	// a few sanity tests
+	if ((n_time != n_elem_by_time*n_time_ch) || (n_val != n_elem_by_val*n_val_ch) || 
+	    (n_time_ch == 0 && n_time > 0) || (n_val_ch == 0 && n_val > 0) ||
+	    (n_time_ch > 0 && n_time == 0) || (n_val_ch > 0 && n_val == 0) || 
+		(n_time_ch > 0 && n_val_ch > 0 && n_elem_by_time != n_elem_by_val))
+	{
+		MERR("ERROR: InMemRepData: non matching time/value numbers for pid %d, sid %d : needed (%d,%d) per element , got (%d,%d) ...\n",
+			pid, sid, n_time_ch, n_val_ch, n_time, n_val);
+		return -1;
+	}
+	int n_elem = max(n_elem_by_time, n_elem_by_val);
+
+	int len_bytes = sigs.Sid2Info[sid].bytes_len;
+
+	vector<char> elem(static_cast<size_t>(len_bytes) * static_cast<size_t>(n_elem));
+
+	int type = sigs.Sid2Info[sid].type;
+
+	//MLOG("pid %d sid %d type %d len_bytes %d nelem %d\n", pid, sid, type, len_bytes, n_elem);
+	int *tdata = time_data;
+	float *vdata = val_data;
+
+	if (n_time_ch == 0) tdata = NULL;
+	if (n_val_ch == 0) vdata = NULL;
+
+	//MLOG("pid %d sid %d type %d len_bytes %d nelem %d\n", pid, sid, type, len_bytes, n_elem);
+	if (type == T_Generic) {
+		GenericSigVec gsv;
+		gsv.init(sigs.Sid2Info[sid]);
+		gsv.set_data(&elem[0], n_elem);
+		for (int i = 0; i < n_elem; i++) {
+			gsv.Set(i, tdata, vdata);
+			if (tdata) tdata += n_time_ch;
+			if (vdata) vdata += n_val_ch;
+		}
+	}
+	else {
+		for (int i = 0; i < n_elem; i++) {
+			if (MedSignalsSingleElemFill(type, &elem[static_cast<size_t>(len_bytes) * static_cast<size_t>(i)], tdata, vdata) < 0) {
+				MERR("ERROR: InMemRepData::insertData failed fill element %d/%d.", i, n_elem);
+				return -1;
+			}
+
+			if (tdata) tdata += n_time_ch;
+			if (vdata) vdata += n_val_ch;
+		}
+	}
+	// all is ready -> we push it to the map
+	pair<int, int> pid_sid(pid, sid);
+	pair<int, vector<char>> n_data;
+	if (data.find(pid_sid) == data.end()) {
+		data[pid_sid] = n_data;
+		data[pid_sid].second = elem;
+		data[pid_sid].first = n_elem;
+		//MLOG("inserted pid %d sid %d nelem %d bytes %d size %d\n", pid, sid, n_elem, len_bytes, elem.size());
+	}
+	else {
+		data[pid_sid].second.insert(data[pid_sid].second.end(), elem.begin(), elem.end());
+		data[pid_sid].first += n_elem;
+	}
+
+	return 0;
+}
+
+//-------------------------------------------------------------------------------------------------------------------
+int InMemRepData::insertData(int pid, const char *sig, int *time_data, float *val_data, int n_time, int n_val)
+{
+	int sid = my_rep->sigs.sid(string(sig));
+	if (sid < 0) {
+		MERR("ERROR: InMemRepData: sig %s in not is signals file (did you read the file\?\?)\n", sig);
+		return -1;
+	}
+	return insertData(pid, sid, time_data, val_data, n_time, n_val);
+
+}
+
+//-------------------------------------------------------------------------------------------------------------------
+int InMemRepData::insertData(int pid, int sid, int *time_data, float *val_data, int n_time, int n_val)
+{
+	return InMemRepData::insertData_to_buffer(pid, sid, time_data, val_data, n_time, n_val, my_rep->sigs, data);
+}
+
+//-------------------------------------------------------------------------------------------------------------------
+int InMemRepData::sort_pid_sid(int pid, int sid)
+{
+	pair<int, int> pid_sid(pid, sid);
+
+	if (data.find(pid_sid) == data.end()) return 0; // nothing to do.
+
+	if (data[pid_sid].first <= 1) return 0; // no need to sort a single variable
+
+	int (*compare_func)(const void *, const void *);
+	GenericSigVec gsv;
+	switch (my_rep->sigs.Sid2Info[sid].type) {
+	case T_Value:				compare_func = &MedSignalsCompareSig<SVal>;				break;
+	case T_DateVal:				compare_func = &MedSignalsCompareSig<SDateVal>;			break;
+	case T_TimeVal:				compare_func = &MedSignalsCompareSig<STimeVal>;			break;
+	case T_DateRangeVal:		compare_func = &MedSignalsCompareSig<SDateRangeVal>;	break;
+	case T_TimeStamp:			compare_func = &MedSignalsCompareSig<STimeStamp>;		break;
+	case T_TimeRangeVal:		compare_func = &MedSignalsCompareSig<STimeRangeVal>;	break;
+	case T_DateVal2:			compare_func = &MedSignalsCompareSig<SDateVal2>;		break;
+	case T_TimeLongVal:			compare_func = &MedSignalsCompareSig<STimeLongVal>;		break;
+	case T_DateShort2:			compare_func = &MedSignalsCompareSig<SDateShort2>;		break;
+	case T_ValShort2:			compare_func = &MedSignalsCompareSig<SValShort2>;		break;
+	case T_ValShort4:			compare_func = &MedSignalsCompareSig<SValShort4>;		break;
+	case T_DateRangeVal2:		compare_func = &MedSignalsCompareSig<SDateRangeVal2>;	break;
+	case T_DateFloat2:			compare_func = &MedSignalsCompareSig<SDateFloat2>;		break;
+	case T_TimeShort4:			compare_func = &MedSignalsCompareSig<STimeShort4>;		break;
+	case T_Generic:
+		gsv.init(my_rep->sigs.Sid2Info[sid]);
+		gsv.inplace_sort_data(&data[pid_sid].second[0], data[pid_sid].first);
+		return 0;
+	//case T_CompactDateVal:		break; // not fully supported yet
+	default: MERR("ERROR:sort_pid_sid Unknown sig_type %d\n", my_rep->sigs.Sid2Info[sid].type);
+		return -1;
+	}
+
+	//MLOG("pid %d sid %d len %d bytes %d first_val %f\n", pid, sid, data[pid_sid].first, my_rep->sigs.Sid2Info[sid].bytes_len, data[pid_sid].second[0]);
+	qsort(&data[pid_sid].second[0], data[pid_sid].first, my_rep->sigs.Sid2Info[sid].bytes_len, compare_func);
+
+	return 0;
+}
+
+//-------------------------------------------------------------------------------------------------------------------
+int InMemRepData::sortData()
+{
+	for (auto &data_elem : data) {
+		//MLOG("Now sorting pid %d sid %d (%s)\n", data_elem.first.first, data_elem.first.second, my_rep->sigs.Sid2Name[data_elem.first.second].c_str());
+		if (sort_pid_sid(data_elem.first.first, data_elem.first.second) < 0) {
+			MERR("FAILED:: InMemRepData::sortData() failed sorting pid %d sid %d\n", data_elem.first.first, data_elem.first.second);
+			return -1;
+		}
+	}
+	return 0;
+}
+
+//-------------------------------------------------------------------------------------------------------------------
+void *InMemRepData::get_from_buffer(int pid, int sid, int &len, const map<pair<int, int>, pair<int, vector<char>>> &data) {
+	pair<int, int> pid_sid(pid, sid);
+	if (data.find(pid_sid) == data.end()) {
+		len = 0;
+		return NULL;
+	}
+
+	len = data.at(pid_sid).first;
+	return (void *)&data.at(pid_sid).second[0];
+}
+
+void * InMemRepData::get(int pid, int sid, int &len)
+{
+	return InMemRepData::get_from_buffer(pid, sid, len, data);
+}
+
+void InMemRepData::erase_pid_data(int pid) {
+	//Erase from data all (pid, sid):
+	for ( auto &it : my_rep->sigs.Name2Sid) {
+		pair<int, int> pid_sid(pid, it.second);
+		if (data.find(pid_sid) != data.end()) {
+			data.erase(pid_sid);
+		}
+	}
+
 }