From df834830ced2f4ee2ae82a963fd94efbce898b0b Mon Sep 17 00:00:00 2001 From: Steven Zeltmann Date: Fri, 14 Mar 2025 10:18:28 -0400 Subject: [PATCH 1/3] fix numpy 2 errors with: ruff check py4DSTEM --select NPY201 --fix --- .../io/legacy/legacy13/v13_emd_classes/io.py | 34 +++++++++---------- .../process/classification/featurization.py | 2 +- py4DSTEM/process/utils/elliptical_coords.py | 4 +-- 3 files changed, 20 insertions(+), 20 deletions(-) diff --git a/py4DSTEM/io/legacy/legacy13/v13_emd_classes/io.py b/py4DSTEM/io/legacy/legacy13/v13_emd_classes/io.py index ddbea9005..0452a5854 100644 --- a/py4DSTEM/io/legacy/legacy13/v13_emd_classes/io.py +++ b/py4DSTEM/io/legacy/legacy13/v13_emd_classes/io.py @@ -127,42 +127,42 @@ def Metadata_to_h5(metadata, group): # None if v is None: v = "_None" - v = np.string_(v) # convert to byte string + v = np.bytes_(v) # convert to byte string dset = grp.create_dataset(k, data=v) - dset.attrs["type"] = np.string_("None") + dset.attrs["type"] = np.bytes_("None") # strings elif isinstance(v, str): - v = np.string_(v) # convert to byte string + v = np.bytes_(v) # convert to byte string dset = grp.create_dataset(k, data=v) - dset.attrs["type"] = np.string_("string") + dset.attrs["type"] = np.bytes_("string") # bools elif isinstance(v, bool): dset = grp.create_dataset(k, data=v, dtype=bool) - dset.attrs["type"] = np.string_("bool") + dset.attrs["type"] = np.bytes_("bool") # numbers elif isinstance(v, Number): dset = grp.create_dataset(k, data=v, dtype=type(v)) - dset.attrs["type"] = np.string_("number") + dset.attrs["type"] = np.bytes_("number") # arrays elif isinstance(v, np.ndarray): dset = grp.create_dataset(k, data=v, dtype=v.dtype) - dset.attrs["type"] = np.string_("array") + dset.attrs["type"] = np.bytes_("array") # tuples elif isinstance(v, tuple): # of numbers if isinstance(v[0], Number): dset = grp.create_dataset(k, data=v) - dset.attrs["type"] = np.string_("tuple") + dset.attrs["type"] = np.bytes_("tuple") # of tuples elif any([isinstance(v[i], tuple) for i in range(len(v))]): dset_grp = grp.create_group(k) - dset_grp.attrs["type"] = np.string_("tuple_of_tuples") + dset_grp.attrs["type"] = np.bytes_("tuple_of_tuples") dset_grp.attrs["length"] = len(v) for i, x in enumerate(v): dset_grp.create_dataset(str(i), data=x) @@ -170,7 +170,7 @@ def Metadata_to_h5(metadata, group): # of arrays elif isinstance(v[0], np.ndarray): dset_grp = grp.create_group(k) - dset_grp.attrs["type"] = np.string_("tuple_of_arrays") + dset_grp.attrs["type"] = np.bytes_("tuple_of_arrays") dset_grp.attrs["length"] = len(v) for i, ar in enumerate(v): dset_grp.create_dataset(str(i), data=ar, dtype=ar.dtype) @@ -178,10 +178,10 @@ def Metadata_to_h5(metadata, group): # of strings elif isinstance(v[0], str): dset_grp = grp.create_group(k) - dset_grp.attrs["type"] = np.string_("tuple_of_strings") + dset_grp.attrs["type"] = np.bytes_("tuple_of_strings") dset_grp.attrs["length"] = len(v) for i, s in enumerate(v): - dset_grp.create_dataset(str(i), data=np.string_(s)) + dset_grp.create_dataset(str(i), data=np.bytes_(s)) else: er = f"Metadata only supports writing tuples with numeric and array-like arguments; found type {type(v[0])}" @@ -192,12 +192,12 @@ def Metadata_to_h5(metadata, group): # of numbers if isinstance(v[0], Number): dset = grp.create_dataset(k, data=v) - dset.attrs["type"] = np.string_("list") + dset.attrs["type"] = np.bytes_("list") # of arrays elif isinstance(v[0], np.ndarray): dset_grp = grp.create_group(k) - dset_grp.attrs["type"] = np.string_("list_of_arrays") + dset_grp.attrs["type"] = np.bytes_("list_of_arrays") dset_grp.attrs["length"] = len(v) for i, ar in enumerate(v): dset_grp.create_dataset(str(i), data=ar, dtype=ar.dtype) @@ -205,10 +205,10 @@ def Metadata_to_h5(metadata, group): # of strings elif isinstance(v[0], str): dset_grp = grp.create_group(k) - dset_grp.attrs["type"] = np.string_("list_of_strings") + dset_grp.attrs["type"] = np.bytes_("list_of_strings") dset_grp.attrs["length"] = len(v) for i, s in enumerate(v): - dset_grp.create_dataset(str(i), data=np.string_(s)) + dset_grp.create_dataset(str(i), data=np.bytes_(s)) else: er = f"Metadata only supports writing lists with numeric and array-like arguments; found type {type(v[0])}" @@ -490,7 +490,7 @@ def PointList_to_h5(pointlist, group): # Add data for f, t in zip(pointlist.fields, pointlist.types): group_current_field = grp.create_dataset(f, data=pointlist.data[f]) - group_current_field.attrs.create("dtype", np.string_(t)) + group_current_field.attrs.create("dtype", np.bytes_(t)) # group_current_field.create_dataset( # "data", # data = pointlist.data[f] diff --git a/py4DSTEM/process/classification/featurization.py b/py4DSTEM/process/classification/featurization.py index 126583413..08dd702de 100644 --- a/py4DSTEM/process/classification/featurization.py +++ b/py4DSTEM/process/classification/featurization.py @@ -967,7 +967,7 @@ def _gmm_single(x, cv, components, num_models, random_seed=None, return_all=True gmm_list = [] gmm_labels = [] gmm_proba = [] - lowest_bic = np.infty + lowest_bic = np.inf bic_temp = 0 if random_seed is None: rng = np.random.RandomState(seed=42) diff --git a/py4DSTEM/process/utils/elliptical_coords.py b/py4DSTEM/process/utils/elliptical_coords.py index 97291bc20..ea72ae390 100644 --- a/py4DSTEM/process/utils/elliptical_coords.py +++ b/py4DSTEM/process/utils/elliptical_coords.py @@ -320,8 +320,8 @@ def elliptical_resample( # Get (qx,qy) corresponding to the coordinates distorted by the ellipse xr, yr = np.mgrid[0:Nx, 0:Ny] - xr0 = xr.astype(np.float_) - qx0 - yr0 = yr.astype(np.float_) - qy0 + xr0 = xr.astype(np.float64) - qx0 + yr0 = yr.astype(np.float64) - qy0 xr = xr0 * np.cos(-theta) - yr0 * np.sin(-theta) yr = xr0 * np.sin(-theta) + yr0 * np.cos(-theta) qx = qx0 + xr * np.cos(theta) - yr * (b / a) * np.sin(theta) From bea0daba72927a4da25d00102fabad224b641f10 Mon Sep 17 00:00:00 2001 From: Steven Zeltmann Date: Fri, 14 Mar 2025 10:20:51 -0400 Subject: [PATCH 2/3] remove numpy restriction in setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 8919e53e8..7e410e20e 100644 --- a/setup.py +++ b/setup.py @@ -23,7 +23,7 @@ keywords="STEM,4DSTEM", python_requires=">=3.10", install_requires=[ - "numpy >= 1.19, < 2.0", + "numpy >= 1.19", "scipy >= 1.5.2", "h5py >= 3.2.0", "hdf5plugin >= 4.1.3", From 23035635e0a0546cdb05bb7b49b8633ff4f6f4f2 Mon Sep 17 00:00:00 2001 From: Steve Zeltmann Date: Fri, 14 Mar 2025 14:58:44 -0400 Subject: [PATCH 3/3] unpin ncempy version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 7e410e20e..8f0107324 100644 --- a/setup.py +++ b/setup.py @@ -27,7 +27,7 @@ "scipy >= 1.5.2", "h5py >= 3.2.0", "hdf5plugin >= 4.1.3", - "ncempy >= 1.8.1, <= 1.11.2", + "ncempy >= 1.8.1", "matplotlib >= 3.2.2", "scikit-image >= 0.17.2", "scikit-learn >= 0.23.2, < 1.5",