Merge branch 'master' of github.com:cryoem/eman2

libEM/io/hdfio2.cpp

@@ -1458,7 +1458,7 @@ int HdfIO2::write_header(const Dict & dict, int image_index, const Region* area,
 }
 
 template<EMUtil::EMDataType I>
-auto HdfIO2::write(float *data, size_t size, hid_t ds, hid_t memoryspace, hid_t filespace) {
+auto HdfIO2::write_compressed(float *data, size_t size, hid_t ds, hid_t memoryspace, hid_t filespace) {
 	auto [rendered_data, rendertrunc] = getRenderedDataAndRendertrunc<typename EM2Type<I>::type>(data, size);
 
 	auto err_no = H5Dwrite(ds, EM2HDF[I], memoryspace, filespace, H5P_DEFAULT, rendered_data.data());
@@ -1469,12 +1469,6 @@ auto HdfIO2::write(float *data, size_t size, hid_t ds, hid_t memoryspace, hid_t
 	return std::make_tuple(I != EMUtil::EM_FLOAT, rendertrunc);
 }
 
-auto HdfIO2::write_compressed(float *data, hsize_t size, hid_t ds, hid_t spc1, hid_t spc2) {
-	if (renderbits<=0)      return write<EMUtil::EM_FLOAT>(data, size, ds, spc1, spc2);
-	else if (renderbits<=8) return write<EMUtil::EM_UCHAR>(data, size, ds, spc1, spc2);
-	else                    return write<EMUtil::EM_USHORT>(data, size, ds, spc1, spc2);
-}
-
 // Writes the actual image data to the corresponding dataset (already created)
 int HdfIO2::write_data(float *data, int image_index, const Region* area,
 					  EMUtil::EMDataType dt, bool)
@@ -1498,7 +1492,6 @@ int HdfIO2::write_data(float *data, int image_index, const Region* area,
 	sprintf(ipath, "/MDF/images/%d/image", image_index);
 
 	// Now create the image dataspace (not used for region writing)
-	hsize_t rank = 0;
 	if (nz == 1 && ny == 1)  {
 		hsize_t dims[1]= { nx };
 		spc=H5Screate_simple(1,dims,NULL);
@@ -1575,6 +1568,7 @@ int HdfIO2::write_data(float *data, int image_index, const Region* area,
 		
 	}
 	
+	hsize_t rank = 0;
 	if (ds < 0) {	//new dataset
 		hid_t plist = H5Pcreate(H5P_DATASET_CREATE);	// we could just use H5P_DEFAULT for non-compressed
 		if (dt==EMUtil::EM_COMPRESSED) {
@@ -1616,9 +1610,6 @@ int HdfIO2::write_data(float *data, int image_index, const Region* area,
 	// convert data to unsigned short, unsigned char...
 	hsize_t size = (hsize_t)nx*ny*nz;
 
-	EMUtil::getRenderMinMax(data, nx, ny, rendermin, rendermax, renderbits, nz);
-//	printf("RMM  %f  %f\n",rendermin,rendermax);
-
 	hid_t filespace = 0;
 	hid_t memoryspace = 0;
 
@@ -1680,27 +1671,26 @@ int HdfIO2::write_data(float *data, int image_index, const Region* area,
 		}
 	}
 
+	hid_t spc1 = (area ? memoryspace : spc);
+	hid_t spc2 = (area ? filespace : spc);
 
-	hid_t spc1 = 0;
-	hid_t spc2 = 0;
-	if (area) {
-		spc1 = memoryspace;
-		spc2 = filespace;
-	}
-	else {
-		spc1 = spc;
-		spc2 = spc;
+	EMUtil::getRenderMinMax(data, nx, ny, rendermin, rendermax, renderbits, nz);
+//	printf("RMM  %f  %f\n",rendermin,rendermax);
+
+	if(dt == EMUtil::EM_COMPRESSED) {
+		if (renderbits <= 0)      dt = EMUtil::EM_FLOAT;
+		else if (renderbits <= 8) dt = EMUtil::EM_UCHAR;
+		else                      dt = EMUtil::EM_USHORT;
 	}
 
 	int rendertrunc = 0;	// keep track of truncated pixels
 	bool scaled = 0;		// set if the data will need rescaling upon read
 	switch(dt) {
-		case EMUtil::EM_FLOAT:      std::tie(scaled, rendertrunc) = write<EMUtil::EM_FLOAT>(data, size, ds, spc1, spc2); break;
-		case EMUtil::EM_SHORT:      std::tie(scaled, rendertrunc) = write<EMUtil::EM_SHORT>(data, size, ds, spc1, spc2); break;
-		case EMUtil::EM_USHORT:     std::tie(scaled, rendertrunc) = write<EMUtil::EM_USHORT>(data, size, ds, spc1, spc2); break;
-		case EMUtil::EM_CHAR:       std::tie(scaled, rendertrunc) = write<EMUtil::EM_CHAR>(data, size, ds, spc1, spc2); break;
-		case EMUtil::EM_UCHAR:      std::tie(scaled, rendertrunc) = write<EMUtil::EM_UCHAR>(data, size, ds, spc1, spc2); break;
-		case EMUtil::EM_COMPRESSED: std::tie(scaled, rendertrunc) = write_compressed(data, size, ds, spc1, spc2); break;
+		case EMUtil::EM_FLOAT:  std::tie(scaled, rendertrunc) = write_compressed<EMUtil::EM_FLOAT>(data, size, ds, spc1, spc2); break;
+		case EMUtil::EM_SHORT:  std::tie(scaled, rendertrunc) = write_compressed<EMUtil::EM_SHORT>(data, size, ds, spc1, spc2); break;
+		case EMUtil::EM_USHORT: std::tie(scaled, rendertrunc) = write_compressed<EMUtil::EM_USHORT>(data, size, ds, spc1, spc2); break;
+		case EMUtil::EM_CHAR:   std::tie(scaled, rendertrunc) = write_compressed<EMUtil::EM_CHAR>(data, size, ds, spc1, spc2); break;
+		case EMUtil::EM_UCHAR:  std::tie(scaled, rendertrunc) = write_compressed<EMUtil::EM_UCHAR>(data, size, ds, spc1, spc2); break;
 		default:
 			throw ImageWriteException(filename,"HDF5 does not support this data format");
 	}

libEM/io/hdfio2.h

@@ -129,8 +129,7 @@ namespace EMAN
 
 	  private:
 		template<EMUtil::EMDataType I>
-		auto write(float *data, size_t size, hid_t ds, hid_t memoryspace, hid_t filespace);
-		auto write_compressed(float *data, hsize_t size, hid_t ds, hid_t spc1, hid_t spc2);
+		auto write_compressed(float *data, size_t size, hid_t ds, hid_t memoryspace, hid_t filespace);
 
 	  private:
 		hsize_t nx, ny, nz;

libpyEM/qtgui/emannotate2d.py

@@ -497,7 +497,7 @@ class EMAnnotate2DWidget(EMGLWidget):
 
 	def register_scroll_motion(self,x,y,z=0):
 		if self.list_data!=None:
-			self.image_range_changed(z)
+			self.ns_changed(z)
 			#self.setup_shapes()
 		animation = LineAnimation(self,self.origin,(x*self.scale-old_div(self.width(),2),y*self.scale-old_div(self.height(),2)))
 		self.qt_parent.register_animatable(animation)
@@ -1013,7 +1013,6 @@ class EMAnnotate2DWidget(EMGLWidget):
 	def inspector_update(self):
 		if not self.inspector is None and not self.data is None:
 			self.inspector.set_limits(self.minden,self.maxden,self.curmin,self.curmax)
-			self.inspector.set_gamma(self.gamma)
 
 			self.inspector.set_scale(self.scale)
 			self.inspector.update_brightness_contrast()
@@ -1864,7 +1863,7 @@ class EMAnnotateInspector2D(QtWidgets.QWidget):
 	def update_zrange(self):
 		nz=self.target().get_data()["nz"]
 		zr=nz*3//4		# approximate max z range with high tilt
-		self.image_range.setRange(-zr,zr)
+		self.ns.setRange(-zr,zr)
 		self.stminsb.setRange(-zr,zr)
 		self.stminsb.setValue(-nz)
 		self.stmaxsb.setRange(-zr,zr)
@@ -2068,7 +2067,7 @@ class EMAnnotateInspector2D(QtWidgets.QWidget):
 		self.pyout.setText(str(r))
 
 	def set_image_idx(self,val,quiet=0):
-		self.image_range.setValue(val,quiet=quiet)
+		self.ns.setValue(val,quiet=quiet)
 
 	def get_contrast(self):
 		return float(self.conts.getValue())
@@ -2088,9 +2087,6 @@ class EMAnnotateInspector2D(QtWidgets.QWidget):
 	def set_minden(self,value,quiet=1):
 		self.mins.setValue(value,quiet)
 
-	def set_gamma(self,value,quiet=1):
-		self.gammas.setValue(value,quiet)
-
 	def set_scale(self,val):
 		if self.busy : return
 		self.busy=1
@@ -2123,11 +2119,6 @@ class EMAnnotateInspector2D(QtWidgets.QWidget):
 		self.update_min_max()
 		self.busy=0
 
-	def new_gamma(self,val):
-		if self.busy : return
-		self.busy=1
-		self.target().set_gamma(val)
-		self.busy=0
 
 	def update_brightness_contrast(self):
 		b=0.5*(self.mins.value+self.maxs.value-(self.lowlim+self.highlim))/((self.highlim-self.lowlim))