New MM::StorageDevice and addition to the MMCore API

DeviceAdapters/go2scope/AcqZarrStorage.h

@@ -0,0 +1,92 @@
+///////////////////////////////////////////////////////////////////////////////
+// FILE:          AcqZarrStorage.h
+// PROJECT:       Micro-Manager
+// SUBSYSTEM:     DeviceAdapters
+//-----------------------------------------------------------------------------
+// DESCRIPTION:   Go2Scope devices. Includes the experimental StorageDevice
+//
+// AUTHOR:        Nenad Amodaj
+//
+// COPYRIGHT:     Nenad Amodaj, Chan Zuckerberg Initiative, 2024
+//
+// LICENSE:       This file is distributed under the BSD license.
+//                License text is included with the source distribution.
+//
+//                This file is distributed in the hope that it will be useful,
+//                but WITHOUT ANY WARRANTY; without even the implied warranty
+//                of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+//
+//                IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+//                CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+//                INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES.
+//
+// NOTE:          Storage Device development is supported in part by
+//                Chan Zuckerberg Initiative (CZI)
+// 
+///////////////////////////////////////////////////////////////////////////////
+
+#pragma once
+#include "MMDevice.h"
+#include "DeviceBase.h"
+
+struct ZarrStream_s;
+
+class AcqZarrStorage : public CStorageBase<AcqZarrStorage>
+{
+public:
+   AcqZarrStorage();
+   virtual ~AcqZarrStorage();
+
+   // Device API
+   // ----------
+   int Initialize();
+   int Shutdown();
+
+   void GetName(char* pszName) const;
+   bool Busy();
+
+   // Storage API
+   // -----------
+   int Create(const char* path, const char* name, int numberOfDimensions, const int shape[], MM::StorageDataType pixType, const char* meta, int metaLength, int* handle);
+   int ConfigureDimension(int handle, int dimension, const char* name, const char* meaning);
+   int ConfigureCoordinate(int handle, int dimension, int coordinate, const char* name);
+   int Close(int handle);
+   int Load(const char* path, int* handle);
+   int GetShape(int handle, int shape[]);
+   int GetDataType(int handle, MM::StorageDataType& pixelDataType) { return dataType; }
+
+   int Delete(int handle);
+   int List(const char* path, char** listOfDatasets, int maxItems, int maxItemLength);
+   int AddImage(int handle, int sizeInBytes, unsigned char* pixels, int coordinates[], int numCoordinates, const char* imageMeta, int metaLength);
+   int AppendImage(int handle, int sizeInBytes, unsigned char* pixels, const char* imageMeta, int metaLength);
+   int GetSummaryMeta(int handle, char** meta);
+   int GetImageMeta(int handle, int coordinates[], int numCoordinates, char** meta);
+   const unsigned char* GetImage(int handle, int coordinates[], int numCoordinates);
+   int GetNumberOfDimensions(int handle, int& numDimensions);
+   int GetDimension(int handle, int dimension, char* name, int nameLength, char* meaning, int meaningLength);
+   int GetCoordinate(int handle, int dimension, int coordinate, char* name, int nameLength);
+	int GetImageCount(int handle, int& imgcnt);
+   bool IsOpen(int handle);
+	bool IsReadOnly(int handle);
+   int GetPath(int handle, char* path, int maxPathLength);
+	int SetCustomMetadata(int handle, const char* key, const char* content, int contentLength) { return DEVICE_UNSUPPORTED_COMMAND; }
+	int GetCustomMetadata(int handle, const char* key, char** content) { return DEVICE_UNSUPPORTED_COMMAND; }
+
+
+   // action interface
+   // ----------------
+
+private:
+   bool initialized;
+   ZarrStream_s* zarrStream;
+   std::vector<int> streamDimensions;
+   MM::StorageDataType dataType;
+   std::vector<int> currentCoordinate;
+   int currentImageNumber;
+   int streamHandle;
+   std::string getErrorMessage(int code);
+   void destroyStream();
+   int ConvertToZarrType(MM::StorageDataType type);
+   std::string streamPath;
+};
+

DeviceAdapters/go2scope/CFileUtil.cpp

@@ -0,0 +1,113 @@
+///////////////////////////////////////////////////////////////////////////////
+// FILE:          G2SFileUtil.cpp
+// PROJECT:       Micro-Manager
+// SUBSYSTEM:     DeviceAdapters
+//-----------------------------------------------------------------------------
+// DESCRIPTION:   Go2Scope devices. Includes the experimental StorageDevice
+//
+// AUTHOR:        Milos Jovanovic <milos@tehnocad.rs>
+//
+// COPYRIGHT:     Nenad Amodaj, Chan Zuckerberg Initiative, 2024
+//
+// LICENSE:       This file is distributed under the BSD license.
+//                License text is included with the source distribution.
+//
+//                This file is distributed in the hope that it will be useful,
+//                but WITHOUT ANY WARRANTY; without even the implied warranty
+//                of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+//
+//                IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+//                CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+//                INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES.
+//
+// NOTE:          Storage Device development is supported in part by
+//                Chan Zuckerberg Initiative (CZI)
+// 
+///////////////////////////////////////////////////////////////////////////////
+#include "G2SFileUtil.h"
+
+/**
+ * Write integer value to a byte buffer
+ * @param buff Byte buffer
+ * @param len Value length (in bytes)
+ * @param val Integer value
+ * @author Miloš Jovanović <milos@tehnocad.rs>
+ * @version 1.0
+ */
+void writeInt(unsigned char* buff, std::uint8_t len, std::uint64_t val) noexcept
+{
+	if(buff == nullptr || len == 0)
+		return;
+	for(auto i = 0; i < len; i++)
+		buff[i] = (val >> (i * 8)) & 0xff;
+}
+
+/**
+ * Read integer value from a byte buffer
+ * @param buff Byte buffer
+ * @param len Value length (in bytes)
+ * @return Integer value
+ * @author Miloš Jovanović <milos@tehnocad.rs>
+ * @version 1.0
+ */
+std::uint64_t readInt(const unsigned char* buff, std::uint8_t len) noexcept
+{
+	if(buff == nullptr || len == 0 || len > 8)
+		return 0;
+	std::uint64_t ret = 0;
+	for(std::uint8_t i = 0; i < len; i++)
+	{
+		auto shift = i * 8;
+		std::uint64_t xval = (std::uint64_t)buff[i] << shift;
+		ret |= xval;
+	}
+	return ret;
+}
+
+/**
+ * Split CSV line into tokens
+ * @param line CSV line
+ * @return Tokens list
+ */
+std::vector<std::string> splitLineCSV(const std::string& line) noexcept
+{
+	std::vector<std::string> ret;
+	if(line.empty())
+		return ret;
+
+	std::string curr = "";
+	bool qopen = false;
+	int qcnt = 0;
+	for(char c : line)
+	{
+		bool endswithQ = curr.size() >= 1 && curr[curr.size() - 1] == '\"';
+		bool endswithS = curr.size() >= 1 && curr[curr.size() - 1] == ' ';
+		bool endswithEQ = curr.size() >= 2 && curr[curr.size() - 1] == '\"' && curr[curr.size() - 1] == '\\';
+		if(c == ',' && (!qopen || (qcnt % 2 == 0 && (endswithQ || endswithS) && !endswithEQ)))
+		{
+			if(curr.size() >= 2 && curr[0] == '\"' && curr[curr.size() - 1] == '\"')
+				curr = curr.substr(1, curr.size() - 2);
+			ret.push_back(curr);
+			curr = "";
+			qcnt = 0;
+			qopen = false;
+		}
+		else if(c == '"')
+		{
+			if(qcnt == 0)
+				qopen = true;
+			qcnt++;
+			//if(qcnt > 1 && qcnt % 2 == 1)
+			curr += "\"";
+		}
+		else
+			curr += c;
+	}
+	if(!curr.empty())
+	{
+		if(curr.size() >= 2 && curr[0] == '\"' && curr[curr.size() - 1] == '\"')
+			curr = curr.substr(1, curr.size() - 2);
+		ret.push_back(curr);
+	}
+	return ret;
+}