Changed module name no lowercase because that's really how it should be

examples/MIT_BNL_logo.py

@@ -1,11 +1,11 @@
-import CDTools
+import cdtools
 from matplotlib import pyplot as plt
 
 
 # This file is too large to be distributed via Github.
 # Please contact Abe Levitan (alevitan@mit) if you would like access
-filename = '/media/Data Bank/CSX_6_17/Processed_CXIs/79511_p.cxi'
-dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(filename)
+filename = '79511_p.cxi'
+dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename)
 
 # In this dataset, the edges of the patterns are masked off anyway
 # We can easily just remove this data instead of leaving it to float.
@@ -18,7 +18,7 @@ dataset.mask = dataset.mask[70:-70,70:-70]
 # translations_scale defines how aggressive the position reconstruction is
 # n_modes is the number of incoherent modes
 # propagation_distance is the distance to propagate from the SHARP-style guess of the probe's focal spot (in this case, the value comes from knowledge of the experimental geometry).
-model = CDTools.models.FancyPtycho.from_dataset(dataset,
+model = cdtools.models.FancyPtycho.from_dataset(dataset,
                                                 translation_scale = 4,
                                                 n_modes=2,
                                                 propagation_distance=73e-6)

examples/basic_ptycho_dataset.py

@@ -1,8 +1,8 @@
 import numpy as np
 import torch as t
 from matplotlib import pyplot as plt
-from CDTools.datasets import CDataset
-from CDTools.tools import data as cdtdata
+from cdtools.datasets import CDataset
+from cdtools.tools import data as cdtdata
 
 
 __all__ = ['BasicPtychoDataset']

examples/ensemble_analysis.py

@@ -1,8 +1,8 @@
 from matplotlib import pyplot as plt
 from scipy import io
 
-from CDTools.tools import plotting
-from CDTools.tools import analysis
+from cdtools.tools import plotting
+from cdtools.tools import analysis
 
 
 

examples/ensemble_reconstruction.py

@@ -1,10 +1,10 @@
-import CDTools
+import cdtools
 import numpy as np
 from scipy import io
 
 # Load the data
 filename = 'example_data/AuBalls_700ms_30nmStep_3_6SS_filter.cxi'
-dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(filename)
+dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename)
 
 results = []
 n = 25
@@ -13,7 +13,7 @@ for idx in range(n):
     print('Starting Reconstruction', idx+1, 'of',n)
     
     # Create a new model each time
-    model = CDTools.models.FancyPtycho.from_dataset(dataset,n_modes=3,
+    model = cdtools.models.FancyPtycho.from_dataset(dataset,n_modes=3,
                                                     randomize_ang=0.1*np.pi)
 
     # Work on the GPU

examples/gold_ball_ptycho.py

@@ -1,14 +1,14 @@
-import CDTools
+import cdtools
 from matplotlib import pyplot as plt
 from scipy import io
 
 # First, we load an example dataset from a .cxi file
 filename = 'example_data/AuBalls_700ms_30nmStep_3_6SS_filter.cxi'
-dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(filename)
+dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename)
 
 # Next, we create a ptychography model from the dataset
 # Note that we explicitly ask for two incoherent probe modes
-model = CDTools.models.FancyPtycho.from_dataset(dataset, n_modes=2)
+model = cdtools.models.FancyPtycho.from_dataset(dataset, n_modes=2)
 
 # Let's do this reconstruction on the GPU, shall we? 
 model.to(device='cuda')

examples/inspect_dataset.py

@@ -1,9 +1,9 @@
-import CDTools
+import cdtools
 from matplotlib import pyplot as plt
 
 # First, we load an example dataset from a .cxi file
 filename = 'example_data/AuBalls_700ms_30nmStep_3_6SS_filter.cxi'
-dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(filename)
+dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename)
 
 # And we take a look at the data
 dataset.inspect()

examples/lab_bragg_2d_ptycho.py

@@ -1,4 +1,4 @@
-import CDTools
+import cdtools
 from matplotlib import pyplot as plt
 from scipy import io
 
@@ -10,12 +10,12 @@ from scipy import io
 
 # This file is too large to be distributed via Github.
 # Please contact Abe Levitan (alevitan@mit) if you would like access
-filename = '/media/Data Bank/Lab Ptycho/Zone Plate Bragg 633.cxi'
-dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(filename)
+filename = 'Zone Plate Bragg 633.cxi'
+dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename)
 
 #dataset.inspect()
 
-model = CDTools.models.Bragg2DPtycho.from_dataset(dataset,probe_support_radius=60,correct_tilt=False)
+model = cdtools.models.Bragg2DPtycho.from_dataset(dataset,probe_support_radius=60,correct_tilt=False)
 model.to(device='cuda')
 dataset.get_as(device='cuda')
 

examples/lab_ptycho_data.py

@@ -1,16 +1,16 @@
-import CDTools
+import cdtools
 from matplotlib import pyplot as plt
 from scipy import io
 
 
 # A simple dataset collected from our optical setup
 filename = 'example_data/lab_ptycho_data.cxi'
-dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(filename)
+dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename)
 
 dataset.inspect(units='mm')
 plt.show()
 
-model = CDTools.models.FancyPtycho.from_dataset(dataset, oversampling=2,
+model = cdtools.models.FancyPtycho.from_dataset(dataset, oversampling=2,
                                                 probe_support_radius=90,
                                                 n_modes=2,
                                                 dm_rank=0,units='mm')

examples/simple_ptycho.py

@@ -1,12 +1,12 @@
-import CDTools
+import cdtools
 from matplotlib import pyplot as plt
 
 # First, we load an example dataset from a .cxi file
 filename = 'example_data/lab_ptycho_data.cxi'
-dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(filename)
+dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename)
 
 # Next, we create a ptychography model from the dataset
-model = CDTools.models.SimplePtycho.from_dataset(dataset)
+model = cdtools.models.SimplePtycho.from_dataset(dataset)
 
 # Now, we run a short reconstruction from the dataset!
 for loss in model.Adam_optimize(20, dataset):

examples/simple_ptycho_model.py

@@ -1,7 +1,7 @@
 import numpy as np
 import torch as t
-from CDTools.models import CDIModel
-from CDTools import tools
+from cdtools.models import CDIModel
+from cdtools import tools
 
 __all__ = ['SimplePtycho']
 

examples/specular_ptycho.py

@@ -1,4 +1,4 @@
-import CDTools
+import cdtools
 from matplotlib import pyplot as plt
 import numpy as np
 
@@ -6,7 +6,7 @@ import numpy as np
 # This file is too large to be distributed via Github.
 # Please contact Abe Levitan (alevitan@mit) if you would like access
 filename = '/media/Data Bank/CSX_10_18/Processed_CXIs/110531_p.cxi'
-dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(filename)
+dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename)
 
 
 # This model definition includes lots of tweaks, described below.
@@ -14,7 +14,7 @@ dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(filename)
 # randomize_ang defines the initial random phase noise's extent
 # translations_scale defines how aggressive the position reconstruction is
 # scattering_mode overrides any sample normal information stored in the .cxi file
-model = CDTools.models.FancyPtycho.from_dataset(dataset,
+model = cdtools.models.FancyPtycho.from_dataset(dataset,
                                                 randomize_ang = np.pi/4,
                                                 translation_scale=10,
                                                 scattering_mode='reflection')

examples/transmission_RPI.py

@@ -1,4 +1,4 @@
-import CDTools
+import cdtools
 import pickle
 from matplotlib import pyplot as plt
 
@@ -11,12 +11,12 @@ with open('example_data/Optical_ptycho_incoherent.pickle', 'rb') as f:
 probe = ptycho_results['probe']
 background = ptycho_results['background']
 
-dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(ss_filename)
+dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(ss_filename)
 
 
 # Next, we create an RPI model from the dataset
 # Note that we explicitly as for two incoherent probe modes
-model = CDTools.models.RPI.from_dataset(dataset, probe, [500,500],
+model = cdtools.models.RPI.from_dataset(dataset, probe, [500,500],
                                         background=background, n_modes=2,
                                         initialization='random')
 

examples/unified_modes.py

@@ -1,10 +1,10 @@
-import CDTools
+import cdtools
 from matplotlib import pyplot as plt
 from scipy import io
 
 
 filename = 'example_data/lab_ptycho_data.cxi'
-dataset = CDTools.datasets.Ptycho2DDataset.from_cxi(filename)
+dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(filename)
 
 #dataset.inspect(units='mm')
 #plt.show()

setup.py

@@ -4,21 +4,21 @@ with open("README.md", "r") as fh:
     long_description = fh.read()
 
 setuptools.setup(
-    name="CDTools",
-    version="0.1.1",
+    name="cdtools",
+    version="0.2.0",
     python_requires='>3.7', # recommended minimum version for pytorch
     author="Abe Levitan",
     author_email="alevitan@mit.edu",
-    description="Coherent Diffraction Tools",
+    description="Tools for coherent diffractive imaging and ptychography",
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.mit.edu/scattering/CDTools.git",
     install_requires=[
         "numpy>=1.0",
         "scipy>=1.0",
-        "matplotlib>=2.0", # 2.0 introduces better colormaps which are used by default
+        "matplotlib>=2.0", # 2.0 has better colormaps which are used by default
         "python-dateutil",
-        "torch>=1.9.0", #1.9.0 implements support for autograd on indexed complex tensors
+        "torch>=1.9.0", #1.9.0 supports autograd on indexed complex tensors
         "h5py>=2.1"],
     extras_require={
         'tests': ["pytest"],

src/CDTools/__init__.py

@@ -6,7 +6,7 @@ warnings.filterwarnings("ignore",
 
 __all__ = ['tools', 'datasets', 'models']
 
-from CDTools import tools
-from CDTools import datasets
-from CDTools import models
+from cdtools import tools
+from cdtools import datasets
+from cdtools import models
 

src/CDTools/datasets/__init__.py

@@ -29,6 +29,6 @@ dataset before attempting to do so
 # to be explicit that import * is safe
 __all__ = ['CDataset','Ptycho2DDataset','PolarizedPtycho2DDataset']
 
-from CDTools.datasets.base import CDataset
-from CDTools.datasets.ptycho_2d_dataset import Ptycho2DDataset
-from CDTools.datasets.polarized_ptycho_2d_dataset import PolarizedPtycho2DDataset
+from cdtools.datasets.base import CDataset
+from cdtools.datasets.ptycho_2d_dataset import Ptycho2DDataset
+from cdtools.datasets.polarized_ptycho_2d_dataset import PolarizedPtycho2DDataset

src/CDTools/datasets/base.py

@@ -17,7 +17,7 @@ import torch as t
 from copy import copy
 import h5py
 import pathlib
-from CDTools.tools import data as cdtdata
+from cdtools.tools import data as cdtdata
 from torch.utils import data as torchdata
 
 __all__ = ['CDataset']

src/CDTools/datasets/polarized_ptycho_2d_dataset.py

@@ -2,9 +2,9 @@ import numpy as np
 import torch as t
 import h5py
 import pathlib
-from CDTools.datasets import Ptycho2DDataset
-from CDTools.tools import data as cdtdata
-from CDTools.tools import plotting
+from cdtools.datasets import Ptycho2DDataset
+from cdtools.tools import data as cdtdata
+from cdtools.tools import plotting
 
 __all__ = ['PolarizedPtycho2DDataset']
 

src/CDTools/datasets/ptycho_2d_dataset.py

@@ -3,9 +3,9 @@ import torch as t
 from copy import copy
 import h5py
 import pathlib
-from CDTools.datasets import CDataset
-from CDTools.tools import data as cdtdata
-from CDTools.tools import plotting
+from cdtools.datasets import CDataset
+from cdtools.tools import data as cdtdata
+from cdtools.tools import plotting
 
 __all__ = ['Ptycho2DDataset']
 

src/CDTools/models/__init__.py

@@ -24,17 +24,17 @@ defining a new ptychography model before attempting to do so.
 # to be explicit that import * is safe
 __all__ = ['CDIModel', 'SimplePtycho', 'FancyPtycho', 'PolarizedFancyPtycho', 'Bragg2DPtycho', 'Multislice2DPtycho', 'RPI', 'TimeResolvedPtychoCalibration', 'TimeResolvedRPI']
 
-from CDTools.models.base import CDIModel
-from CDTools.models.simple_ptycho import SimplePtycho
-from CDTools.models.fancy_ptycho import FancyPtycho
-from CDTools.models.polarized_fancy_ptycho import PolarizedFancyPtycho
-from CDTools.models.bragg_2d_ptycho import Bragg2DPtycho
-from CDTools.models.multislice_2d_ptycho import Multislice2DPtycho
-from CDTools.models.rpi import RPI
-from CDTools.models.multimode_rpi import MultimodeRPI
-from CDTools.models.time_resolved_ptycho_calibration import TimeResolvedPtychoCalibration
-from CDTools.models.time_resolved_rpi import TimeResolvedRPI
+from cdtools.models.base import CDIModel
+from cdtools.models.simple_ptycho import SimplePtycho
+from cdtools.models.fancy_ptycho import FancyPtycho
+from cdtools.models.polarized_fancy_ptycho import PolarizedFancyPtycho
+from cdtools.models.bragg_2d_ptycho import Bragg2DPtycho
+from cdtools.models.multislice_2d_ptycho import Multislice2DPtycho
+from cdtools.models.rpi import RPI
+from cdtools.models.multimode_rpi import MultimodeRPI
+from cdtools.models.time_resolved_ptycho_calibration import TimeResolvedPtychoCalibration
+from cdtools.models.time_resolved_rpi import TimeResolvedRPI
 
 # Still needs to be updated for the new complex numbers
-#from CDTools.models.s_matrix_ptycho import SMatrixPtycho
+#from cdtools.models.s_matrix_ptycho import SMatrixPtycho
 

src/CDTools/models/bragg_2d_ptycho.py

@@ -1,9 +1,9 @@
 import torch as t
-from CDTools.models import CDIModel
-from CDTools.datasets import Ptycho2DDataset
-from CDTools import tools
-from CDTools.tools import plotting as p
-from CDTools.tools.propagators import generate_generalized_angular_spectrum_propagator as ggasp
+from cdtools.models import CDIModel
+from cdtools.datasets import Ptycho2DDataset
+from cdtools import tools
+from cdtools.tools import plotting as p
+from cdtools.tools.propagators import generate_generalized_angular_spectrum_propagator as ggasp
 from matplotlib import pyplot as plt
 from datetime import datetime
 import numpy as np
@@ -455,7 +455,7 @@ class Bragg2DPtycho(CDIModel):
         
         # First, I need to gather all the relevant data
         # that needs to be added to the dataset
-        entry_info = {'program_name': 'CDTools',
+        entry_info = {'program_name': 'cdtools',
                       'instrument_n': 'Simulated Data',
                       'start_time': datetime.now()}
 

src/CDTools/models/fancy_ptycho.py

@@ -1,9 +1,9 @@
 import torch as t
-from CDTools.models import CDIModel
-from CDTools.datasets import Ptycho2DDataset
-from CDTools import tools
-from CDTools.tools import plotting as p
-from CDTools.tools import analysis
+from cdtools.models import CDIModel
+from cdtools.datasets import Ptycho2DDataset
+from cdtools import tools
+from cdtools.tools import plotting as p
+from cdtools.tools import analysis
 from matplotlib import pyplot as plt
 from datetime import datetime
 import numpy as np
@@ -414,7 +414,7 @@ class FancyPtycho(CDIModel):
 
         # First, I need to gather all the relevant data
         # that needs to be added to the dataset
-        entry_info = {'program_name': 'CDTools',
+        entry_info = {'program_name': 'cdtools',
                       'instrument_n': 'Simulated Data',
                       'start_time': datetime.now()}
 

src/CDTools/models/multimode_rpi.py

@@ -1,9 +1,9 @@
 import torch as t
-from CDTools.models import CDIModel
-from CDTools import tools
-from CDTools.tools import plotting as p
-from CDTools.tools.interactions import RPI_interaction
-from CDTools.tools import initializers
+from cdtools.models import CDIModel
+from cdtools import tools
+from cdtools.tools import plotting as p
+from cdtools.tools.interactions import RPI_interaction
+from cdtools.tools import initializers
 from scipy.ndimage.morphology import binary_dilation
 import numpy as np
 from copy import copy

src/CDTools/models/multislice_2d_ptycho.py

@@ -1,9 +1,9 @@
 import torch as t
-from CDTools.models import CDIModel
-from CDTools.datasets import Ptycho2DDataset
-from CDTools import tools
-from CDTools.tools import analysis, image_processing
-from CDTools.tools import plotting as p
+from cdtools.models import CDIModel
+from cdtools.datasets import Ptycho2DDataset
+from cdtools import tools
+from cdtools.tools import analysis, image_processing
+from cdtools.tools import plotting as p
 from matplotlib import pyplot as plt
 from datetime import datetime
 import numpy as np
@@ -447,7 +447,7 @@ class Multislice2DPtycho(CDIModel):
         
         # First, I need to gather all the relevant data
         # that needs to be added to the dataset
-        entry_info = {'program_name': 'CDTools',
+        entry_info = {'program_name': 'cdtools',
                       'instrument_n': 'Simulated Data',
                       'start_time': datetime.now()}
 

src/CDTools/models/polarized_fancy_ptycho.py

@@ -1,16 +1,16 @@
 import torch as t
-from CDTools.models import CDIModel, FancyPtycho
-from CDTools.datasets import Ptycho2DDataset
-from CDTools import tools
-from CDTools.tools import plotting as p
-# from CDTools.tools import polarized_plotting as pp
-from CDTools.tools import analysis
+from cdtools.models import CDIModel, FancyPtycho
+from cdtools.datasets import Ptycho2DDataset
+from cdtools import tools
+from cdtools.tools import plotting as p
+# from cdtools.tools import polarized_plotting as pp
+from cdtools.tools import analysis
 from matplotlib import pyplot as plt
 from datetime import datetime
 import numpy as np
 from scipy import linalg as sla
 from copy import copy
-from CDTools.tools import polarization
+from cdtools.tools import polarization
 
 __all__ = ['PolarizedFancyPtycho']
 
@@ -353,7 +353,7 @@ class PolarizedFancyPtycho(FancyPtycho):
 
         # First, I need to gather all the relevant data
         # that needs to be added to the dataset
-        entry_info = {'program_name': 'CDTools',
+        entry_info = {'program_name': 'cdtools',
                       'instrument_n': 'Simulated Data',
                       'start_time': datetime.now()}
 

src/CDTools/models/rpi.py

@@ -1,9 +1,9 @@
 import torch as t
-from CDTools.models import CDIModel
-from CDTools import tools
-from CDTools.tools import plotting as p
-from CDTools.tools.interactions import RPI_interaction
-from CDTools.tools import initializers
+from cdtools.models import CDIModel
+from cdtools import tools
+from cdtools.tools import plotting as p
+from cdtools.tools.interactions import RPI_interaction
+from cdtools.tools import initializers
 from scipy.ndimage.morphology import binary_dilation
 import numpy as np
 from copy import copy

src/CDTools/models/s_matrix_ptycho.py

@@ -1,9 +1,9 @@
 import torch as t
-from CDTools.models import CDIModel
-from CDTools.datasets import Ptycho2DDataset
-from CDTools import tools
-from CDTools.tools import cmath
-from CDTools.tools import plotting as p
+from cdtools.models import CDIModel
+from cdtools.datasets import Ptycho2DDataset
+from cdtools import tools
+from cdtools.tools import cmath
+from cdtools.tools import plotting as p
 from matplotlib import pyplot as plt
 from datetime import datetime
 import numpy as np
@@ -353,7 +353,7 @@ class SMatrixPtycho(CDIModel):
         
         # First, I need to gather all the relevant data
         # that needs to be added to the dataset
-        entry_info = {'program_name': 'CDTools',
+        entry_info = {'program_name': 'cdtools',
                       'instrument_n': 'Simulated Data',
                       'start_time': datetime.now()}
 

src/CDTools/models/simple_ptycho.py

@@ -1,8 +1,8 @@
 import torch as t
-from CDTools.models import CDIModel
-from CDTools.datasets import Ptycho2DDataset
-from CDTools import tools
-from CDTools.tools import plotting as p
+from cdtools.models import CDIModel
+from cdtools.datasets import Ptycho2DDataset
+from cdtools import tools
+from cdtools.tools import plotting as p
 from copy import copy
 from torch.utils import data as torchdata
 from datetime import datetime
@@ -159,7 +159,7 @@ class SimplePtycho(CDIModel):
 
         # First, I need to gather all the relevant data
         # that needs to be added to the dataset
-        entry_info = {'program_name': 'CDTools',
+        entry_info = {'program_name': 'cdtools',
                       'instrument_n': 'Simulated Data',
                       'start_time': datetime.now()}
 

src/CDTools/models/time_resolved_ptycho_calibration.py

@@ -1,9 +1,9 @@
 import torch as t
-from CDTools.models import CDIModel
-from CDTools.datasets import Ptycho2DDataset
-from CDTools import tools
-from CDTools.tools import plotting as p
-from CDTools.tools import analysis
+from cdtools.models import CDIModel
+from cdtools.datasets import Ptycho2DDataset
+from cdtools import tools
+from cdtools.tools import plotting as p
+from cdtools.tools import analysis
 from matplotlib import pyplot as plt
 from datetime import datetime
 import numpy as np
@@ -362,7 +362,7 @@ class TimeResolvedPtychoCalibration(CDIModel):
 
         # First, I need to gather all the relevant data
         # that needs to be added to the dataset
-        entry_info = {'program_name': 'CDTools',
+        entry_info = {'program_name': 'cdtools',
                       'instrument_n': 'Simulated Data',
                       'start_time': datetime.now()}
 

src/CDTools/models/time_resolved_rpi.py

@@ -1,9 +1,9 @@
 import torch as t
-from CDTools.models import CDIModel
-from CDTools import tools
-from CDTools.tools import plotting as p
-from CDTools.tools.interactions import RPI_interaction
-from CDTools.tools import initializers
+from cdtools.models import CDIModel
+from cdtools import tools
+from cdtools.tools import plotting as p
+from cdtools.tools.interactions import RPI_interaction
+from cdtools.tools import initializers
 from scipy.ndimage.morphology import binary_dilation
 import numpy as np
 from copy import copy

src/CDTools/tools/__init__.py

@@ -9,19 +9,19 @@ that one needs for a specific application.
 The submodules are all structured as modules with their own __init__ files,
 which use an import * statement to import from a file defining the various
 functions. This is done to prevent leakage of imported packages into the
-namespace of CDTools. I know, we're all consenting adults, but I just hate
-having numpy and torch defined under CDTools.tools.cmath, you know?
+namespace of cdtools. I know, we're all consenting adults, but I just hate
+having numpy and torch defined under cdtools.tools.cmath, you know?
 
 """
 
-from CDTools.tools import losses
-from CDTools.tools import data
-from CDTools.tools import image_processing
-from CDTools.tools import initializers
-from CDTools.tools import plotting
-from CDTools.tools import interactions
-from CDTools.tools import propagators
-from CDTools.tools import measurements
-from CDTools.tools import analysis
-from CDTools.tools import atoms
-from CDTools.tools import polarization
+from cdtools.tools import losses
+from cdtools.tools import data
+from cdtools.tools import image_processing
+from cdtools.tools import initializers
+from cdtools.tools import plotting
+from cdtools.tools import interactions
+from cdtools.tools import propagators
+from cdtools.tools import measurements
+from cdtools.tools import analysis
+from cdtools.tools import atoms
+from cdtools.tools import polarization

src/CDTools/tools/analysis/__init__.py

@@ -1 +1 @@
-from CDTools.tools.analysis.analysis import *
+from cdtools.tools.analysis.analysis import *

src/CDTools/tools/analysis/analysis.py

@@ -8,7 +8,7 @@ data has been stored in numpy arrays.
 
 import torch as t
 import numpy as np
-from CDTools.tools import image_processing as ip
+from cdtools.tools import image_processing as ip
 from scipy import fftpack
 from scipy import linalg as sla
 from scipy import special

src/CDTools/tools/atoms/__init__.py

@@ -1 +1 @@
-from CDTools.tools.atoms.atoms import *
+from cdtools.tools.atoms.atoms import *

src/CDTools/tools/data/__init__.py

@@ -1 +1 @@
-from CDTools.tools.data.data import *
+from cdtools.tools.data.data import *

src/CDTools/tools/data/data.py

@@ -419,7 +419,7 @@ def get_ptycho_translations(cxi_file):
     """Gets an array of x,y,z translations, if such an array has been defined in the file
 
     It negates the translations, because the CXI file format is designed
-    to specify translations of the samples and the CDTools code specifies
+    to specify translations of the samples and the cdtools code specifies
     translations of the optics.
 
     Parameters
@@ -775,7 +775,7 @@ def add_ptycho_translations(cxi_file, translations):
         The translations to be saved
     """
     # accounting for the different definition between cxi files and
-    # CDTools
+    # cdtools
     translations = -translations
 
     add_shot_to_shot_info(cxi_file, translations, 'translation')

src/CDTools/tools/image_processing/__init__.py

@@ -1 +1 @@
-from CDTools.tools.image_processing.image_processing import *
+from cdtools.tools.image_processing.image_processing import *

src/CDTools/tools/image_processing/image_processing.py

@@ -9,7 +9,7 @@ a way that it is safe to include them in automatic differentiation models.
 
 import numpy as np
 import torch as t
-from CDTools.tools import propagators
+from cdtools.tools import propagators
 
 __all__ = ['centroid', 'centroid_sq', 'sinc_subpixel_shift',
            'find_subpixel_shift', 'find_pixel_shift', 'find_shift',

src/CDTools/tools/initializers/__init__.py

@@ -1 +1 @@
-from CDTools.tools.initializers.initializers import *
+from cdtools.tools.initializers.initializers import *

src/CDTools/tools/initializers/initializers.py

@@ -8,9 +8,9 @@ geierating sensible initializations for the probe guess.
 import math
 import numpy as np
 import torch as t
-from CDTools.tools.propagators import *
-from CDTools.tools.analysis import orthogonalize_probes
-from CDTools.tools import image_processing
+from cdtools.tools.propagators import *
+from cdtools.tools.analysis import orthogonalize_probes
+from cdtools.tools import image_processing
 from scipy.fftpack import next_fast_len
 from scipy.sparse import linalg as spla
 from torch.nn.functional import pad

src/CDTools/tools/interactions/__init__.py

@@ -1 +1 @@
-from CDTools.tools.interactions.interactions import *
+from cdtools.tools.interactions.interactions import *

src/CDTools/tools/interactions/interactions.py

@@ -7,7 +7,7 @@ for ptychographic reconstruction.
 
 import torch as t
 import numpy as np
-from CDTools.tools import propagators, image_processing, polarization
+from cdtools.tools import propagators, image_processing, polarization
 
 __all__ = ['translations_to_pixel', 'pixel_to_translations',
            'project_translations_to_sample',

src/CDTools/tools/losses/__init__.py

@@ -1 +1 @@
-from CDTools.tools.losses.losses import *
+from cdtools.tools.losses.losses import *

src/CDTools/tools/measurements/__init__.py

@@ -1 +1 @@
-from CDTools.tools.measurements.measurements import *
+from cdtools.tools.measurements.measurements import *

src/CDTools/tools/plotting/__init__.py

@@ -1,2 +1,2 @@
-from CDTools.tools.plotting.plotting import *
+from cdtools.tools.plotting.plotting import *
 

src/CDTools/tools/polarization/__init__.py

@@ -1 +1 @@
-from CDTools.tools.polarization.polarization import *
+from cdtools.tools.polarization.polarization import *

src/CDTools/tools/propagators/__init__.py

@@ -1 +1 @@
-from CDTools.tools.propagators.propagators import *
+from cdtools.tools.propagators.propagators import *

tests/conftest.py

@@ -51,7 +51,7 @@ def ptycho_cxi_1():
     e1f['experiment_identifier'] = np.string_(e1e['experiment_identifier'])
     e1e['experiment_description'] = 'A fully defined ptychography experiment to test the data loading'
     e1f['experiment_description'] = np.string_(e1e['experiment_description'])
-    e1e['program_name'] = 'CDTools'
+    e1e['program_name'] = 'cdtools'
     e1f['program_name'] = np.string_(e1e['program_name'])
     e1e['title'] = 'The one experiment we did'
     e1f['title'] = np.string_(e1e['title'])

tests/test_datasets.py

@@ -1,5 +1,5 @@
-from CDTools.datasets import *
-from CDTools.tools import data as cdtdata
+from cdtools.datasets import *
+from cdtools.tools import data as cdtdata
 import numpy as np
 import torch as t
 import h5py

tests/tools/test_analysis.py

@@ -4,7 +4,7 @@ from scipy import linalg as la
 import torch as t
 from itertools import combinations
 
-from CDTools.tools import analysis, initializers
+from cdtools.tools import analysis, initializers
 
 
 def test_orthogonalize_probes():

tests/tools/test_data.py

@@ -1,4 +1,4 @@
-from CDTools.tools import data
+from cdtools.tools import data
 import numpy as np
 import torch as t
 import h5py

tests/tools/test_image_processing.py

@@ -1,7 +1,7 @@
 import numpy as np
 import torch as t
 
-from CDTools.tools import image_processing, interactions
+from cdtools.tools import image_processing, interactions
 from scipy import ndimage
 
 def test_centroid():

tests/tools/test_initializers.py

@@ -1,5 +1,5 @@
-from CDTools.tools import initializers
-from CDTools.datasets import Ptycho2DDataset
+from cdtools.tools import initializers
+from cdtools.datasets import Ptycho2DDataset
 import numpy as np
 import torch as t
 

tests/tools/test_interactions.py

@@ -1,4 +1,4 @@
-from CDTools.tools import interactions
+from cdtools.tools import interactions
 import numpy as np
 import torch as t
 from numpy import fft

tests/tools/test_losses.py

@@ -1,4 +1,4 @@
-from CDTools.tools import losses
+from cdtools.tools import losses
 import numpy as np
 import torch as t
 

tests/tools/test_measurements.py

@@ -1,4 +1,4 @@
-from CDTools.tools import measurements
+from cdtools.tools import measurements
 import torch as t
 import numpy as np
 

tests/tools/test_plotting.py

@@ -1,5 +1,5 @@
-from CDTools.tools import plotting
-from CDTools.tools import initializers
+from cdtools.tools import plotting
+from cdtools.tools import initializers
 import numpy as np
 import torch as t
 import scipy.misc

tests/tools/test_polarization.py

@@ -1,7 +1,7 @@
 import numpy as np
 import torch as t
-from CDTools.tools.polarization import apply_linear_polarizer, generate_linear_polarizer
-from CDTools.tools.polarization import apply_jones_matrix as jones
+from cdtools.tools.polarization import apply_linear_polarizer, generate_linear_polarizer
+from cdtools.tools.polarization import apply_jones_matrix as jones
 
 
 # Abe - I removed all the imports that didn't need to be here.
@@ -621,4 +621,4 @@ def test_apply_jones_matrix_mult_modes_one_pattern_probe_mult_patterns_jones_2()
     assert t.allclose(out[2, 3, 1, :-2, -2:], t.zeros(2, 2, dtype=t.cfloat))
     assert t.allclose(out[2, 3, 0, -2:, :-2], out[2, 3, 1, -2:, :-2])
     assert np.allclose(np.real(out[2, 3, 0, -2:, -2:]), np.real(out[2, 3, 0, -2:, -2:]))
-    assert out.shape == t.Size((3, 4, 2, 4, 4))
+    assert out.shape == t.Size((3, 4, 2, 4, 4))

tests/tools/test_propagators.py

@@ -1,6 +1,6 @@
-from CDTools.tools import initializers
-from CDTools.tools import propagators
-from CDTools.tools import image_processing
+from cdtools.tools import initializers
+from cdtools.tools import propagators
+from cdtools.tools import image_processing
 
 import numpy as np
 import torch as t