diff --git a/src/Python/_property.py b/src/Python/_property.py
deleted file mode 100644
index 151ce35bea817b2ccae296b1d7c6a2698b293911..0000000000000000000000000000000000000000
--- a/src/Python/_property.py
+++ /dev/null
@@ -1,79 +0,0 @@
-import requests
-import json
-
-
-"""
-Helper classes for handling leversc settings changes
-"""
-class ChangeWrapper:
- """
- A wrapper class for bubbling property change updates to leversc class
- """
- def __init__(self, parent, incollection):
- self._parent = parent
- self._collection = incollection
-
- def _property_updated(self, childprop):
- self._parent._property_updated(self)
-
- def __getitem__(self, keyidx):
- elem = self._collection.__getitem__(keyidx)
- if isinstance(elem, (dict,list)):
- return __class__(self, elem)
- else:
- return elem
-
- def __setitem__(self, keyidx, v):
- self._collection.__setitem__(keyidx,v)
- self._property_updated(self)
-
- """
- Some Quality-of-life improvements for introspecting the wrappers
- """
- def __str__(self):
- return str(self._collection)
-
- def __repr__(self):
- return "%s(%s)"%(__class__.__name__, repr(self._collection))
-
-
-class PropWrapper(ChangeWrapper):
- """
- Top-level property that runs setProperty (network send) on change updates
- """
- def __init__(self, lsc, propname, incollection):
- self._leversc = lsc
- self._propname = propname
- super(__class__,self).__init__(self,incollection)
-
- def unwrap(self):
- """
- Return an unwrapped version of this property (that can be edited without network overhead)
- """
- return self._collection
-
- def _property_updated(self, childprop):
- self._leversc.setProperty(self._propname, self._collection)
-
- def __str__(self):
- return str(self._collection)
-
- def __repr__(self):
- return "%s(%s)"%(__class__.__name__, repr(self._collection))
-
-
-# retrieves/sets viewParams, renderParams, uiParams, etc....
-def setProperty(self,propertyName,propertyStruct):
- if isinstance(propertyStruct,PropWrapper):
- propertyStruct = propertyStruct.unwrap()
- URL = self._leversc_url("/"+propertyName)
- response = requests.post(URL,json=propertyStruct)
-
-def getProperty(self,propertyName):
- URL = self._leversc_url("/"+propertyName)
- response = requests.get(URL)
- property = response.json()
- if 'list'==type(property):
- # view and render params come as 1 element list
- property = property[0]
- return PropWrapper(self,propertyName,property)
diff --git a/src/Python/leversc.py b/src/Python/leversc.py
deleted file mode 100644
index b3fbd6959889187b99c8318dd9129b880f4641b6..0000000000000000000000000000000000000000
--- a/src/Python/leversc.py
+++ /dev/null
@@ -1,396 +0,0 @@
-import math
-import json
-import struct
-import requests
-import numpy as np
-import os
-import sys
-import time
-import pkgutil
-import subprocess
-from imageio import imread
-
-class leversc:
- """
- A class wrapper to interface with the leversc viewer.
-
- This class is built to function similarly to matplotlib and Matlab's figure() function,
- the leversc object represents a single leversc viewer window with associated image metadata (imD)
- and visualization parameters. Object methods allow changing rendering parameters programatically
- and send new images to view (with the same metadata).
-
- Parameters
- ----------
- im : numpy.ndarray, optional
- 5-D image to send to viewer on startup, can also be sent using the show(im) method
- imD : dict, optional
- Leverjs image metadata, can be reset using the setImageData(imD) method
- figNum : int, default=1
- Figure number of the leversc viewer (default to 1)
-
- Raises
- ------
- TypeError
- If im is not None and is not of type numpy.ndarray
-
- See Also
- --------
- show: Show 5-D image in the leversc viewer
- """
- def __init__(self, im=None, imD=None, figNumber=1,strDB=None):
- self._host = "http://localhost"
- self._base_port = 3000
- self._npack = 4
-
- self._figNumber = figNumber
- self.setImageData(imD)
- if strDB is not None:
- self.showLEVER(strDB)
- elif im is not None:
- self.show(im)
-
- def setImageData(self, imD=None):
- """
- Set the image metadata associated with this viewer window.
-
- This function will set or reset (in the case of imD=None or no arguments) the leverjs metadata associated with
- this leversc viewer window.
-
- Parameters
- ----------
- imD : dict, optional
- Leverjs image metadata
- Important Keys:
- "PhysicalPixelSize" - The resolution of each pixel dimension x,y,z (generally in um)
- "ChannelNames" - The names of each channel in the image
- """
- if imD is None:
- self._CONSTANTS={}
- self._imageData = {}
- elif 'imageData' in imD.keys():
- # passed in a CONSTANTS struct - use CONSTANTS.imageData
- self._CONSTANTS=imD
- self._imageData = imD['imageData']
- else:
- self._CONSTANTS={}
- self._imageData = imD
-
-
- def setFigureNumber(self, figNumber):
- """
- Set the the figure number (leversc viewer) associated with this object
-
- Parameters
- ----------
- figNumber : int
- This is the figure number (leversc window) that the object will send images to
-
- Raises
- ------
- ValueError
- If figNumber is less than 1
- """
- if figNumber <= 0:
- raise ValueError("Figure number must be greater than zero")
- self._figNumber = figNumber
-
- def captureImage(self):
- if ( not self._check_leversc() ):
- return None
- # make sure leversc is ready
- while (not self.drawComplete()):
- time.sleep(0.1)
- # do the capture
- URL = self._leversc_url('screenCap')
- im=imread(URL)
- return im
-
- def drawComplete(self):
- URL=self._leversc_url('drawComplete')
- response=requests.get(URL)
- bComplete=response.json()
- return bComplete
- def showLEVER(self,strDB):
- """
- Open a .LEVER file in the leversc viewer
-
- Parameters
- ----------
- strDB : string
- /path/to/myFile.LEVER
-
- """
- if ( not self._check_leversc() ):
- if ( not self._init_leversc(strDB) ):
- return
-
- def show(self, im):
- """
- Show a 5-D image in the leversc viewer
-
- Sends a 5-D numpy array to the leversc viewer for display. Note: if the imageData has not been set
- then this method will set default imageData based on the input image.
-
- Parameters
- ----------
- im : numpy.ndarray
- 5-D image to send to viewer
-
- Raises
- ------
- TypeError
- If im is not of type numpy.ndarray
- """
- if type(im) is not np.ndarray:
- raise TypeError("Image must be a numpy array")
-
- if len(im.shape) < 3:
- print("ERROR: 2D Images are not supported!")
- return
-
- # Launch leversc viewer if not alread up
- if ( not self._check_leversc() ):
- if ( not self._init_leversc() ):
- return
-
- # Normalize image access by creating an f_contiguous image view
- imfctg = leversc._get_fcontig_imview(im)
- if len(imfctg.shape) == 3:
- imfctg = np.expand_dims(imfctg, axis=3)
- # Normalize dimensions (make sure there are at least 4 (x,y,z,c))
- def onepad_slice(tpl, size): return (tpl + (1,)*(size-len(tpl)))
- dims = onepad_slice(imfctg.shape, 4)
-
- if ( len(dims) > 4 and dims[4] > 1 ):
- print('WARNING: Multi-frame images are not supported using frame 1!')
- imfctg = imfctg[:,:,:,:,0]
-
- # Convert im to uint8
- chmax = np.amax(np.amax(np.amax(imfctg, axis=0, keepdims=True), axis=1, keepdims=True), axis=2, keepdims=True)
- chim = ((255.0 * imfctg) / chmax).astype("uint8")
-
- # Setup valid imageData
- self._imageData = leversc._imd_from_im(imfctg,dims,self._imageData)
-
- header_json,count_packs = self._make_header(dims)
-
- # Multipart-post request send
- multipart = [("header", (None, header_json, "application/json"))]
- for i in range(count_packs):
- multipart.append(("lbins",("lbin%d"%(i), self._im_to_lbin(chim,dims,i), "application/octet-stream")))
-
- resp = requests.post(url=self._leversc_url("/loadfig"), files=multipart)
-
- # if we have a CONSTANTS and a renderParams, set it
- if self._CONSTANTS!={} and 'renderParams' in self._CONSTANTS.keys():
- self.renderParams=self._CONSTANTS['renderParams']
-
-
- def _im_to_lbin(self,im,dims,pidx):
- choffset = pidx * self._npack
- chsize = min(dims[3]-choffset, self._npack)
-
- imsub = im[:,:,:,choffset:(choffset+chsize)]
- lbin_size = 4*2 + np.prod(dims[:3])*chsize
-
- outbytes = bytearray(lbin_size)
- struct.pack_into("!HHHH", outbytes, 0, chsize,dims[0],dims[1],dims[2])
- imout = np.frombuffer(memoryview(outbytes)[(4*2):], "uint8")
-
- imout[:] = np.reshape(np.transpose(imsub, (3,0,1,2)), -1, order='F')
- return outbytes
-
-
- def _make_header(self, dims):
- count_packs = math.ceil(dims[3] / self._npack)
-
- # Make json metadata header
- imdjson = json.dumps(self._imageData)
- return imdjson,count_packs
-
- def _check_leversc(self):
- try:
- resp = requests.get(url=self._leversc_url("/info"), timeout=0.5)
- except requests.exceptions.ConnectTimeout as e:
- return False
- except requests.exceptions.ConnectionError as e:
- return False
- except Exception as e:
- print("Unable to contact leversc server: %s (%s)" % (self._leversc_url("/info"), e))
- return False
- return True
-
-
- def _leversc_url(self,reqpath):
- if ('/' != reqpath[0]):
- reqpath='/'+reqpath
- return "%s:%s%s"%(self._host,self._base_port + self._figNumber, reqpath)
-
-
- @staticmethod
- def _get_fcontig_imview(im):
- if im.flags.f_contiguous:
- return im
- else:
- imflat = np.reshape(im, -1, order='A')
- imfctg = np.reshape(imflat, im.shape[::-1], order='F')
- return imfctg
-
-
- @staticmethod
- def _get_normalized_dims(im):
- # Helper to pd im.shape out to required number of dimensions
- def _opad_slice(tpl, size): return (tpl + (1,)*(size-len(tpl)))[:size]
-
- # Reverse the dimension order depending of f/c_contiguous
- if im.flags.f_contiguous:
- # dims = _opad_slice(im.shape, 4)
- dims = _opad_slice(im.shape, 4)
- else:
- dims = _opad_slice(im.shape[::-1], 4)
- return dims
-
-
- @staticmethod
- def _imd_from_im(im, dims, imD):
- # Make sure every channel has a name ("Channel %i" by default)
- chnames = imD["ChannelNames"] if "ChannelNames" in imD else []
- chnames = [chnames[x] if len(chnames) > x else "Channel %s"%(x+1) for x in range(dims[3])]
-
- # Set valid pixel size for each x,y,z dim
- pxsize = imD["PixelPhysicalSize"] if "PixelPhysicalSize" in imD else [1,1,1]
- pxsize = [x if x > 0 else 1 for x in pxsize]
-
- new_imD = {"Dimensions": dims[:3],
- "NumberOfChannels": dims[3],
- "ChannelNames": chnames,
- "PixelPhysicalSize": pxsize,
- "PixelFormat": "uint8"}
- return new_imD
-
-
- def _init_leversc(self,strDB=None):
- leverpath = leversc._get_leverjs_path()
- if ( not self._run_leversc(leverpath,strDB) ):
- return False
-
- # Try to contact leversc after launch
- for _ in range(10):
- time.sleep(0.5)
- if ( self._check_leversc() ):
- return True
-
- print("Unable to contact Leversc app")
- return False
-
-
- def _run_leversc(self, leverpath,strDB):
- runargs = None
- if ( leverpath is None ):
- # Try to run installed leversc from path
- runargs = ["open","-a","leverjs.app","-n","--args"] if leversc._is_macos() else ["leverjs"]
- else:
- runargs = leversc._get_os_ljselectron_exec(leverpath)
-
- if ( runargs is None ):
- print("Unable to start Leversc app")
- return False
-
- if strDB is not None:
- strDB=os.path.abspath(strDB)
- runargs.append("--leverFile=%s" % strDB)
- port = self._base_port + self._figNumber
- runargs.append("--port=%s" % port)
- runargs.append("--title=figure %s" % self._figNumber)
- p = leversc._exec_bg_process(runargs)
- if ( p is None):
- return False
- return True
-
-
- @staticmethod
- def _get_os_ljselectron_exec(leverpath):
- runargs = None
- if ( leversc._is_windows() ):
- elec_path = os.path.join(leverpath,"node_modules","electron","dist","electron.exe")
- mainjs_path = os.path.join(leverpath,"elever","main.js")
- runargs = [elec_path, mainjs_path]
- elif ( leversc._is_linux() or leversc._is_macos() ):
- elec_path = os.path.join(leverpath,"node_modules",".bin","electron")
- mainjs_path = os.path.join(leverpath,"elever","main.js")
- runargs = [elec_path, mainjs_path]
-
- return runargs
-
-
- @staticmethod
- def _exec_bg_process(args):
- try:
- if ( leversc._is_windows() ):
- p = subprocess.Popen(args,
- stdin=subprocess.DEVNULL,
- stdout=subprocess.DEVNULL,
- stderr=subprocess.DEVNULL,
- creationflags=subprocess.CREATE_NEW_PROCESS_GROUP)
- elif ( leversc._is_linux() or leversc._is_macos() ):
- p = subprocess.Popen(args,
- stdin=subprocess.DEVNULL,
- stdout=subprocess.DEVNULL,
- stderr=subprocess.DEVNULL,
- start_new_session=True)
- else:
- return None
- except Exception as e:
- print("Unable to launch leversc: (%s)"%e)
- return None
- return p
-
-
- @staticmethod
- def _is_windows():
- return (sys.platform == "win32")
-
- @staticmethod
- def _is_linux():
- return (sys.platform == "linux" or sys.platform == "cygwin")
-
- @staticmethod
- def _is_macos():
- return (sys.platform == "darwin")
-
-
- @staticmethod
- def _get_leverjs_path():
- # Check if ljspath.py is on sys.path (e.g. PYTHONPATH)
- chk_ldr = pkgutil.find_loader("ljspath")
- if ( chk_ldr is None ):
- return None
- # Try to load the module
- ljs_m = chk_ldr.load_module("ljspath")
- if ( ljs_m is None ):
- return None
- return ljs_m.get_ljspath()
-
- from _readImage import readImage
- from _property import setProperty,getProperty
- @property
- def viewParams(self):
- return self.getProperty('viewParams')
- @viewParams.setter
- def viewParams(self,VP):
- self.setProperty('viewParams',VP)
- @property
- def renderParams(self):
- return self.getProperty('renderParams')
- @renderParams.setter
- def renderParams(self,RP):
- self.setProperty('renderParams',RP)
- @property
- def uiParams(self):
- return self.getProperty('uiParams')
- @uiParams.setter
- def uiParams(self,UIP):
- self.setProperty('uiParams',UIP)
-
-
-
diff --git a/src/Python/leversc/_property.py b/src/Python/leversc/_property.py
index bf7e7a53dc3f4f56ac3481e22f69832acfa264f0..151ce35bea817b2ccae296b1d7c6a2698b293911 100644
--- a/src/Python/leversc/_property.py
+++ b/src/Python/leversc/_property.py
@@ -1,8 +1,71 @@
import requests
import json
+
+"""
+Helper classes for handling leversc settings changes
+"""
+class ChangeWrapper:
+ """
+ A wrapper class for bubbling property change updates to leversc class
+ """
+ def __init__(self, parent, incollection):
+ self._parent = parent
+ self._collection = incollection
+
+ def _property_updated(self, childprop):
+ self._parent._property_updated(self)
+
+ def __getitem__(self, keyidx):
+ elem = self._collection.__getitem__(keyidx)
+ if isinstance(elem, (dict,list)):
+ return __class__(self, elem)
+ else:
+ return elem
+
+ def __setitem__(self, keyidx, v):
+ self._collection.__setitem__(keyidx,v)
+ self._property_updated(self)
+
+ """
+ Some Quality-of-life improvements for introspecting the wrappers
+ """
+ def __str__(self):
+ return str(self._collection)
+
+ def __repr__(self):
+ return "%s(%s)"%(__class__.__name__, repr(self._collection))
+
+
+class PropWrapper(ChangeWrapper):
+ """
+ Top-level property that runs setProperty (network send) on change updates
+ """
+ def __init__(self, lsc, propname, incollection):
+ self._leversc = lsc
+ self._propname = propname
+ super(__class__,self).__init__(self,incollection)
+
+ def unwrap(self):
+ """
+ Return an unwrapped version of this property (that can be edited without network overhead)
+ """
+ return self._collection
+
+ def _property_updated(self, childprop):
+ self._leversc.setProperty(self._propname, self._collection)
+
+ def __str__(self):
+ return str(self._collection)
+
+ def __repr__(self):
+ return "%s(%s)"%(__class__.__name__, repr(self._collection))
+
+
# retrieves/sets viewParams, renderParams, uiParams, etc....
-def setProperty(self,propertyName,propertyStruct):
+def setProperty(self,propertyName,propertyStruct):
+ if isinstance(propertyStruct,PropWrapper):
+ propertyStruct = propertyStruct.unwrap()
URL = self._leversc_url("/"+propertyName)
response = requests.post(URL,json=propertyStruct)
@@ -13,4 +76,4 @@ def getProperty(self,propertyName):
if 'list'==type(property):
# view and render params come as 1 element list
property = property[0]
- return property
+ return PropWrapper(self,propertyName,property)
diff --git a/src/Python/leversc/leversc.py b/src/Python/leversc/leversc.py
index a643794c1ccb892ac18dd97d67b093c421724096..b3fbd6959889187b99c8318dd9129b880f4641b6 100644
--- a/src/Python/leversc/leversc.py
+++ b/src/Python/leversc/leversc.py
@@ -342,7 +342,6 @@ class leversc:
return None
except Exception as e:
print("Unable to launch leversc: (%s)"%e)
- print("please check the app is properly installed. see https://leverjs.net/leversc for details.")
return None
return p
@@ -372,11 +371,11 @@ class leversc:
return None
return ljs_m.get_ljspath()
- from leversc._readImage import readImage
- from leversc._property import setProperty,getProperty
+ from _readImage import readImage
+ from _property import setProperty,getProperty
@property
def viewParams(self):
- return self.getProperty('viewParams')
+ return self.getProperty('viewParams')
@viewParams.setter
def viewParams(self,VP):
self.setProperty('viewParams',VP)