Merge branch 'devel' into olz_volume_consensus

.github/workflows/build.yml

@@ -29,7 +29,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     env:
-      SEND_INSTALLATION_STATISTICS: "False"
+      SEND_INSTALLATION_STATISTICS: OFF
     steps:
       - name: Install dependencies
         run: |

README.md

@@ -15,46 +15,39 @@ This is the main repository, which contains the majority of the source code for
 To have a complete overview about Xmipp please visit the [documentation web](https://i2pc.github.io/docs/). The recommended way for users (not developers) to install and use Xmipp is via the [Scipion](http://scipion.i2pc.es/) framework, where you can use Xmipp with other Cryo-EM-related software. 
 
 ### As a Scipion plugin (Recommended)
-The Scipion installer should take care of all dependencies for you by default, except for CUDA. To correctly interoperate with CUDA, please visit the official [installation guide](https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html#installation) of Scipion.
+
+Mind that for this command to succeed, all dependencies need to be pre-installed and findable by Xmipp. When using non-standard install directories, this needs to be indicated to Xmipp though the Scipion configuration file. See [Software dependency section](https://github.com/I2PC/xmipp?tab=readme-ov-file#software-dependencies) for further details.
+To correctly interoperate with CUDA, please visit the official [installation guide](https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html#installation) of Scipion.
 
 Once Scipion is in working order, launch the Xmipp Plugin installer with
 
 `scipion3 installp -p scipion-em-xmipp`
 
 By default this will employ all CPU cores available in the system for compilation. If this is not the desired behavior, please consider using `-j <N>` flag to limit the amount of CPU cores.
 
-### As a Scipion plugin with pre-installed dependencies
-The former method also installs dependencies (including the compiler) though conda. If you prefer to use externally installed dependencies and avoid downloading them from conda use
-
-`scipion3 installp -p scipion-em-xmipp --noBin`
-
-`scipion3 installb xmippSrc`
-
-Mind that for this command to succeed, all dependencies need to be pre-installed and findable by Xmipp. When using non-standard install directories, this needs to be indicated to Xmipp though the Scipion configuration file. See [Software dependency section](https://github.com/I2PC/xmipp?tab=readme-ov-file#software-dependencies) for further details.
-
 ### Developer installation with Scipion
-For developers, it becomes handy to install Xmipp in an external directory for easy integration with IDEs. By default Xmipp installer takes care of installing dependencies though conda and linking to Scipion.
+For developers, it becomes handy to install Xmipp in an external directory for easy integration with IDEs. By default Xmipp installer takes care of linking to Scipion.
 
 The first step is to download Xmipp sources:
 
 `git clone https://github.com/I2PC/xmipp.git`
 
 `cd xmipp`
 
-Then all child repositories need to be fetched, with an optional git branch parameter. For repositories where the branch does not exist, devel is utilized.
+If you want to checkout an scpecific branch use the following command. For repositories where the branch does not exist, devel is utilized.
 
-`./xmipp getSources [-b branch]`
-
-Install the Scipion plugin and dependencies
-
-`scipion3 installp -p src/scipion-em-xmipp/ --devel`
+`./xmipp getSources -b branch`
 
 Compile Xmipp
 
 `scipion3 run ./xmipp`
 
 Refer to `./xmipp --help` for additional info on the compilation process and possible customizations.
 
+Install the Scipion plugin.
+
+`scipion3 installp -p src/scipion-em-xmipp/ --devel`
+
 #### Integrating with Visual Studio Code
 The CMake based installation script can be tightly integrated with any modern IDE. This section shows the procedure for Visual Studio Code (VSCode).
 

cmake/xmipp.bashrc.in

@@ -6,6 +6,7 @@ export PATH=@XMIPP_HOME@/@CMAKE_INSTALL_BINDIR@:$PATH
 export LD_LIBRARY_PATH=@XMIPP_HOME@/@CMAKE_INSTALL_LIBDIR@:@XMIPP_HOME@/bindings/python:@PREFIX_LIB_PATH@:$LD_LIBRARY_PATH
 export PYTHONPATH=@XMIPP_HOME@/bindings/python:@XMIPP_HOME@/pylib:$PYTHONPATH
 export MATLABPATH=@XMIPP_HOME@/bindings/matlab:$MATLABPATH
+export XMIPP_SRC=@PROJECT_SOURCE_DIR@/src
 
 alias x='xmipp'
 alias xsj='xmipp_showj'

installer/constants/config.py

@@ -54,6 +54,8 @@
 # This is not used in cmake
 __CONDA_PREFIX = 'CONDA_PREFIX'
 __XMIPP_CUDA_BIN = 'XMIPP_CUDA_BIN'
+__DEFAULT_CUDA_BIN = '/usr/local/cuda/bin'
+__NVCC_EXE = 'nvcc'
 __TUNE_FLAG='-mtune=native'
 
 # Config file variable structure
@@ -81,6 +83,25 @@ def __getPrefixPath() -> Optional[str]:
 	"""
 	return os.environ.get(__CONDA_PREFIX)
 
+def __getCudaCompiler() -> Optional[str]:
+	"""
+	### This function returns the path for the CUDA compiller
+
+	#### Returns:
+	- (str | None): Path for the NVCC executable
+	"""
+	nvcc = os.environ.get(__XMIPP_CUDA_BIN)
+
+	if nvcc is None and os.path.exists(__DEFAULT_CUDA_BIN):
+		nvcc = __DEFAULT_CUDA_BIN
+
+	if nvcc is not None:
+		nvcc = os.path.join(nvcc, __NVCC_EXE)
+
+	return nvcc
+
+
+
 ON = 'ON'
 OFF = 'OFF'
 CONFIG_DEFAULT_VALUES = {
@@ -93,7 +114,7 @@ def __getPrefixPath() -> Optional[str]:
 	CMAKE_INSTALL_PREFIX: INSTALL_PATH,
 	__CC_FLAGS: __TUNE_FLAG,
 	__CXX_FLAGS: __TUNE_FLAG,
-	CUDA_COMPILER: None,
+	CUDA_COMPILER: __getCudaCompiler(),
 	__PREFIX_PATH: __getPrefixPath(),
 	__MPI_HOME: None,
 	__PYTHON_HOME: None,

src/xmipp/applications/programs/tomo_average_subtomos/tomo_average_subtomos.cpp

@@ -0,0 +1,28 @@
+/***************************************************************************
+ *
+ * Authors:     J.L. Vilas
+ *
+ * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program 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.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+ * 02111-1307  USA
+ *
+ *  All comments concerning this program package may be sent to the
+ *  e-mail address 'xmipp@cnb.csic.es'
+ ***************************************************************************/
+
+#include <tomo/tomo_average_subtomos.h>
+
+RUN_XMIPP_PROGRAM(ProgAverageSubtomos)

src/xmipp/applications/scripts/denoising_tv/denoising_tv.py

@@ -98,7 +98,7 @@ def tigreDenoisingTV(self):
 
         tomo = mrcfile.read(self.fnTomo)
 
-        denoisedTomo = im_3d_denoise.im3ddenoise(tomo, iter=self.iterations, lmbda=self.lmbda, gpuids=None)
+        denoisedTomo = im_3d_denoise.im3ddenoise(np.array(tomo, dtype=np.float32), iter=self.iterations, lmbda=self.lmbda, gpuids=None)
 
         with mrcfile.new(self.fnOut, overwrite=True) as mrc:
             mrc.set_data(denoisedTomo)
@@ -133,4 +133,4 @@ def readVolTomo(self):
     scipion xmipp_denoising_tv -g 0
     '''
     exitCode=DenoisingTV().tryRun()
-    sys.exit(exitCode)
+    sys.exit(exitCode)