tomwer 1.2.8__py3-none-any.whl → 1.3.0a0__py3-none-any.whl

tomwer/io/utils/raw_and_processed_data.py

@@ -0,0 +1,84 @@
+"""some utils to move a path to process_data or to raw_data"""
+
+import os
+from nxtomomill.converter.hdf5.utils import (
+    RAW_DATA_DIR_NAME,
+    PROCESSED_DATA_DIR_NAME,
+)
+
+
+def to_raw_data_path(file_path: str):
+    """convert a path to 'RAW_DATA' when possible"""
+    split_path = file_path.split(os.sep)
+    # reverse it to find the lower level value of 'PROCESSED_DATA_DIR_NAME' if by any 'chance' has several in the path
+    # in this case this is most likely what we want
+    split_path = split_path[::-1]
+    # check if already contain in a "RAW_DATA_DIR_NAME" directory
+    try:
+        index_raw_data = split_path.index(RAW_DATA_DIR_NAME)
+    except ValueError:
+        index_raw_data = None
+
+    try:
+        index_processed_data = split_path.index(PROCESSED_DATA_DIR_NAME)
+    except ValueError:
+        # if the value is not in the list
+        pass
+    else:
+        if index_raw_data is None or index_raw_data > index_processed_data:
+            # make sure we are not already in a 'PROCESSED_DATA' directory. Not sure it will never happen but safer
+            split_path[index_processed_data] = RAW_DATA_DIR_NAME
+
+    # reorder path to original
+    split_path = split_path[::-1]
+    return os.sep.join(split_path)
+
+
+def to_processed_data_path(file_path: str):
+    """convert a path to 'PROCESSED_DATA' when possible"""
+    split_path = file_path.split(os.sep)
+    # reverse it to find the lower level value of '_RAW_DATA_DIR_NAME' if by any 'chance' has several in the path
+    # in this case this is most likely what we want
+    split_path = split_path[::-1]
+    # check if already contain in a "PROCESSED_DATA" directory
+    try:
+        index_processed_data = split_path.index(PROCESSED_DATA_DIR_NAME)
+    except ValueError:
+        index_processed_data = None
+
+    try:
+        index_raw_data = split_path.index(RAW_DATA_DIR_NAME)
+    except ValueError:
+        # if the value is not in the list
+        pass
+    else:
+        if index_processed_data is None or index_raw_data < index_processed_data:
+            # make sure we are not already in a 'PROCESSED_DATA' directory. Not sure it will never happen but safer
+            split_path[index_raw_data] = PROCESSED_DATA_DIR_NAME
+
+    # reorder path to original
+    split_path = split_path[::-1]
+    return os.sep.join(split_path)
+
+
+def file_is_on_processed_data(file_path: str):
+    """Util that raises an error if path is not in PROCESSED_DATA folder"""
+    split_path = file_path.split(os.sep)
+    # reverse it to find the lower level value of 'PROCESSED_DATA_DIR_NAME' if by any 'chance' has several in the path
+    # in this case this is most likely what we want
+    split_path = split_path[::-1]
+    # check if already contain in a "RAW_DATA_DIR_NAME" directory
+    try:
+        index_raw_data = split_path.index(RAW_DATA_DIR_NAME)
+    except ValueError:
+        index_raw_data = None
+
+    try:
+        index_processed_data = split_path.index(PROCESSED_DATA_DIR_NAME)
+    except ValueError:
+        # if the value is not in the list
+        index_processed_data = None
+    else:
+        if index_raw_data is not None and index_raw_data < index_processed_data:
+            return False
+    return index_processed_data is not None

tomwer/io/utils/tomoobj.py

@@ -36,7 +36,7 @@ def get_tomo_objs_instances(tomo_objs: tuple) -> tuple:
     """
     instances = []
     has_scans = False
-    has_vols = True
+    has_vols = False
     for tomo_obj in tomo_objs:
 
         def get_scans():
@@ -45,9 +45,7 @@ def get_tomo_objs_instances(tomo_objs: tuple) -> tuple:
             except Exception:
                 try:
                     return ScanFactory.create_scan_objects(tomo_obj)
-                except Exception as e:
-                    raise e
-                    print("error is", e)
+                except Exception:
                     return tuple()
 
         def get_volumes():
@@ -68,12 +66,12 @@ def get_tomo_objs_instances(tomo_objs: tuple) -> tuple:
             # we start by scan because they have a 'definition' as NXtomo available.
             # otherwise we might get some entries defined as scan AND volume...
             # for stitching we expect users to ask of for one or the other.
-            volumes = get_volumes()
+            volumes = get_volumes() or ()
             if len(volumes) > 0:
                 has_vols = True
                 instances.extend(volumes)
         else:
-            has_scans = True
+            has_scans = len(scans_found) > 0
             instances.extend(scans_found)
 
     return tuple(instances), (has_scans, has_vols)

tomwer/resources/gui/icons/ruler.svg

@@ -0,0 +1,273 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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+
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+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
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+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg">
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+     pagecolor="#ffffff"
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tomwer/resources/gui/icons/short_description.svg

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tomwer/resources/gui/icons/url.svg

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+         x="0.16326435"
+         y="9.5309248">url</tspan></text>
+  </g>
+</svg>

tomwer/synctools/stacks/edit/darkflatpatch.py

@@ -38,7 +38,7 @@ from tomwer.core.process.edit import darkflatpatch
 from tomwer.core.scan.edfscan import EDFTomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 
 from ..processingstack import FIFO, ProcessingThread
 
@@ -60,7 +60,7 @@ class DarkFlatPatchProcessStack(FIFO, qt.QObject):
         assert isinstance(data, TomwerScanBase)
         self._computationThread.finished.connect(self._end_threaded_computation)
 
-        if isOnLbsram(data) and isLowOnMemory(get_lbsram_path()) is True:
+        if isOnLbsram(data) and is_low_on_memory(get_lbsram_path()) is True:
             # if computer is running into low memory on lbsram skip it
             mess = "low memory, skip dark-flat-patch reconstruction for", data.path
             _logger.processSkipped(mess)

tomwer/synctools/stacks/edit/imagekeyeditor.py

@@ -36,7 +36,7 @@ from silx.gui import qt
 from tomwer.core.process.edit import imagekeyeditor
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 
 from ..processingstack import FIFO, ProcessingThread
 
@@ -57,7 +57,7 @@ class ImageKeyEditorProcessStack(FIFO, qt.QObject):
         assert isinstance(data, TomwerScanBase)
         self._computationThread.finished.connect(self._end_threaded_computation)
 
-        if isOnLbsram(data) and isLowOnMemory(get_lbsram_path()) is True:
+        if isOnLbsram(data) and is_low_on_memory(get_lbsram_path()) is True:
             # if computer is running into low memory on lbsram skip it
             mess = f"low memory, skip image-key-edition for {data.path}"
             _logger.processSkipped(mess)

tomwer/synctools/stacks/reconstruction/axis.py

@@ -37,10 +37,10 @@ from silx.gui import qt
 from tomwer.core.process.reconstruction.axis import AxisTask
 from tomwer.core.process.reconstruction.axis.axis import NoAxisUrl
 from tomwer.core.process.reconstruction.axis.mode import AxisMode
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.synctools.axis import QAxisRP
 
 from ..processingstack import FIFO, ProcessingThread
@@ -70,7 +70,7 @@ class AxisProcessStack(FIFO, qt.QObject):
         self._data_currently_computed = data
         self._axis_params.frame_width = data.dim_1
         mode = self._axis_params.mode
-        if isOnLbsram(data) and isLowOnMemory(get_lbsram_path()) is True:
+        if isOnLbsram(data) and is_low_on_memory(get_lbsram_path()) is True:
             # if computer is running into low memory on lbsram skip it
             mess = "low memory, skip axis calculation", data.path
             ProcessManager().notify_dataset_state(
@@ -92,7 +92,7 @@ class AxisProcessStack(FIFO, qt.QObject):
                 cor = 0
             data._axis_params.set_relative_value(cor)
             cor = data._axis_params.relative_cor_value
-            if isinstance(data, HDF5TomoScan):
+            if isinstance(data, NXtomoScan):
                 entry = data.entry
             else:
                 entry = "entry"

tomwer/synctools/stacks/reconstruction/castvolume.py

@@ -38,7 +38,7 @@ from tomwer.core.process.reconstruction.nabu.castvolume import CastVolumeTask
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
 from tomwer.core.tomwer_object import TomwerObject
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.volume.volumebase import TomwerVolumeBase
 from tomwer.core.volume.volumefactory import VolumeFactory
 
@@ -81,7 +81,7 @@ class CastVolumeProcessStack(FIFO, qt.QObject):
         if (
             path is not None
             and isOnLbsram(path)
-            and isLowOnMemory(get_lbsram_path()) is True
+            and is_low_on_memory(get_lbsram_path()) is True
         ):
             # if computer is running into low memory on lbsram skip it
             mess = f"low memory, skip volume cast {data}"

tomwer/synctools/stacks/reconstruction/dkrefcopy.py

@@ -38,7 +38,7 @@ from silx.gui import qt
 from tomwer.core.process.reconstruction.darkref.darkrefscopy import DarkRefsCopy
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 
 from ..processingstack import FIFO, ProcessingThread
 
@@ -85,7 +85,7 @@ class DarkRefCopyProcessStack(FIFO, qt.QObject):
         _logger.processStarted(f"dk-flat-copy {data}")
         assert isinstance(data, TomwerScanBase)
         self._data_currently_computed = data
-        if isOnLbsram(data) and isLowOnMemory(get_lbsram_path()) is True:
+        if isOnLbsram(data) and is_low_on_memory(get_lbsram_path()) is True:
             # if computer is running into low memory on lbsram skip it
             mess = "low memory, skip dk-flat-copy", data.path
             try:
@@ -107,7 +107,7 @@ class DarkRefCopyProcessStack(FIFO, qt.QObject):
             # need to manage connect before starting it because
             fct_callback = functools.partial(self._end_threaded_computation, callback)
             self._computationThread.finished.connect(fct_callback)
-            self._computationThread.sigRefSetted.connect(self._repeatSigRefSetted)
+            self._computationThread.sigRefSetted.connect(self.sigRefSetted)
             self._computationThread.start()
 
     def _end_computation(self, data, future_tomo_obj, callback):
@@ -132,9 +132,6 @@ class DarkRefCopyProcessStack(FIFO, qt.QObject):
     def _create_processing_thread(self, process_id=None) -> qt.QThread:
         return _ProcessingThread(process_id=process_id, save_dir=self._save_dir)
 
-    def _repeatSigRefSetted(self, *args, **kwargs):
-        self.sigRefSetted.emit(*args, **kwargs)
-
 
 class _ProcessingThread(ProcessingThread, SuperviseProcess):
     """
@@ -167,15 +164,12 @@ class _ProcessingThread(ProcessingThread, SuperviseProcess):
         process = DarkRefsCopyWithSig(
             parent=self.parent(), inputs=inputs, process_id=self.process_id
         )
-        process.sigRefSetted.connect(self._repeatSigRefSetted)
+        process.sigRefSetted.connect(self.sigRefSetted)
         try:
             process.run()
         except Exception as e:
             _logger.warning(e)
 
-    def _repeatSigRefSetted(self, *args, **kwargs):
-        self.sigRefSetted.emit(*args, **kwargs)
-
 
 class DarkRefsCopyWithSig(qt.QObject, DarkRefsCopy):
     sigRefSetted = qt.Signal(str)